Query 022056
Match_columns 303
No_of_seqs 236 out of 1136
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 07:42:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022056.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022056hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0774 Transcription factor P 100.0 5.1E-36 1.1E-40 275.1 18.8 215 31-289 26-249 (334)
2 KOG0773 Transcription factor M 99.9 7.3E-29 1.6E-33 237.8 -1.0 249 33-292 49-303 (342)
3 PF03791 KNOX2: KNOX2 domain ; 99.9 1.9E-23 4.1E-28 150.1 7.2 50 97-150 3-52 (52)
4 PF03790 KNOX1: KNOX1 domain ; 99.8 4.4E-21 9.5E-26 133.7 2.7 43 34-76 1-43 (45)
5 PF05920 Homeobox_KN: Homeobox 99.7 5.1E-17 1.1E-21 111.3 4.6 40 246-285 1-40 (40)
6 PF03792 PBC: PBC domain; Int 99.6 1.2E-14 2.7E-19 129.2 13.8 154 33-227 26-190 (191)
7 cd00086 homeodomain Homeodomai 99.5 1.3E-14 2.9E-19 104.2 6.3 57 230-289 2-58 (59)
8 smart00389 HOX Homeodomain. DN 99.5 3.3E-14 7.2E-19 101.6 6.0 55 230-287 2-56 (56)
9 PF00046 Homeobox: Homeobox do 99.5 2.3E-14 4.9E-19 103.4 5.1 57 229-288 1-57 (57)
10 KOG0775 Transcription factor S 99.3 1.2E-12 2.6E-17 122.0 6.6 81 204-287 132-232 (304)
11 TIGR01565 homeo_ZF_HD homeobox 99.0 3.5E-10 7.6E-15 83.5 4.0 53 228-283 1-57 (58)
12 KOG0843 Transcription factor E 99.0 2.9E-10 6.2E-15 100.7 3.7 62 227-291 101-162 (197)
13 KOG0487 Transcription factor A 99.0 2.9E-10 6.3E-15 108.5 2.7 60 229-291 236-295 (308)
14 KOG0489 Transcription factor z 98.9 6.2E-10 1.3E-14 104.3 3.5 63 228-293 159-221 (261)
15 KOG0493 Transcription factor E 98.9 1.2E-09 2.6E-14 101.7 4.2 59 228-289 246-304 (342)
16 KOG0850 Transcription factor D 98.8 1.6E-09 3.5E-14 99.2 3.3 59 228-289 122-180 (245)
17 KOG0842 Transcription factor t 98.8 1.5E-09 3.2E-14 103.7 2.3 60 227-289 152-211 (307)
18 KOG3802 Transcription factor O 98.8 2.1E-09 4.6E-14 105.0 2.6 67 222-291 288-354 (398)
19 KOG0485 Transcription factor N 98.8 2.5E-09 5.5E-14 97.3 2.8 60 227-289 103-162 (268)
20 KOG0483 Transcription factor H 98.7 6.3E-09 1.4E-13 94.1 3.8 58 229-289 51-108 (198)
21 KOG0488 Transcription factor B 98.7 6.7E-09 1.5E-13 99.7 4.2 60 227-289 171-230 (309)
22 COG5576 Homeodomain-containing 98.7 9.6E-09 2.1E-13 89.8 3.7 62 228-292 51-112 (156)
23 KOG0491 Transcription factor B 98.7 1.2E-08 2.7E-13 89.4 3.8 62 225-289 97-158 (194)
24 KOG0492 Transcription factor M 98.7 9.1E-09 2E-13 93.1 2.3 67 220-289 136-202 (246)
25 KOG0494 Transcription factor C 98.4 1.3E-07 2.8E-12 88.2 3.7 55 232-289 145-199 (332)
26 KOG2251 Homeobox transcription 98.4 1.5E-07 3.2E-12 85.9 3.6 59 228-289 37-95 (228)
27 KOG0484 Transcription factor P 98.4 2.3E-07 4.9E-12 76.0 4.1 58 229-289 18-75 (125)
28 KOG0848 Transcription factor C 98.4 1.3E-07 2.8E-12 88.5 1.3 54 234-290 205-258 (317)
29 KOG0486 Transcription factor P 98.3 2.7E-07 5.8E-12 88.1 2.0 60 228-290 112-171 (351)
30 KOG4577 Transcription factor L 98.1 1.4E-06 3E-11 82.5 2.4 71 221-294 160-230 (383)
31 KOG2252 CCAAT displacement pro 98.1 4.2E-06 9.2E-11 84.9 5.1 56 228-286 420-475 (558)
32 KOG0844 Transcription factor E 98.0 1.3E-06 2.9E-11 83.2 1.1 62 232-296 185-246 (408)
33 KOG0847 Transcription factor, 98.0 3.8E-06 8.1E-11 77.0 2.7 63 228-293 167-229 (288)
34 KOG1168 Transcription factor A 98.0 1.8E-06 3.9E-11 81.8 0.5 64 228-294 309-372 (385)
35 KOG0490 Transcription factor, 97.9 4.6E-06 1E-10 74.9 1.9 63 225-290 57-119 (235)
36 KOG0849 Transcription factor P 97.9 1.1E-05 2.4E-10 78.9 3.8 60 229-291 177-236 (354)
37 KOG0773 Transcription factor M 97.5 6.2E-05 1.3E-09 72.6 3.0 64 229-293 96-159 (342)
38 PF11569 Homez: Homeodomain le 97.5 9.5E-05 2.1E-09 54.3 3.2 43 240-285 10-52 (56)
39 PF03789 ELK: ELK domain ; In 97.0 0.0006 1.3E-08 41.1 2.3 22 206-227 1-22 (22)
40 KOG0490 Transcription factor, 96.0 0.0054 1.2E-07 55.0 3.0 60 228-290 153-212 (235)
41 KOG1146 Homeobox protein [Gene 92.0 0.12 2.5E-06 58.1 3.1 60 228-290 903-962 (1406)
42 PF04218 CENP-B_N: CENP-B N-te 89.7 0.49 1.1E-05 34.0 3.6 47 229-283 1-47 (53)
43 KOG3623 Homeobox transcription 85.3 1.7 3.6E-05 46.7 5.8 48 240-290 568-615 (1007)
44 cd06171 Sigma70_r4 Sigma70, re 79.2 3.2 6.9E-05 27.4 3.6 45 235-287 11-55 (55)
45 PF08281 Sigma70_r4_2: Sigma-7 78.4 3.1 6.8E-05 29.0 3.5 43 235-285 11-53 (54)
46 PF01527 HTH_Tnp_1: Transposas 77.1 3.1 6.7E-05 30.8 3.3 45 231-283 3-48 (76)
47 PF04545 Sigma70_r4: Sigma-70, 77.1 3.2 6.9E-05 28.7 3.2 47 234-288 4-50 (50)
48 cd00569 HTH_Hin_like Helix-tur 75.8 6 0.00013 23.3 3.9 39 233-279 4-42 (42)
49 PRK06759 RNA polymerase factor 65.2 7.9 0.00017 32.1 3.5 47 234-288 106-152 (154)
50 PRK00118 putative DNA-binding 58.9 12 0.00026 30.8 3.4 47 235-289 18-64 (104)
51 TIGR02937 sigma70-ECF RNA poly 56.0 13 0.00029 29.5 3.2 46 235-288 111-156 (158)
52 PRK09642 RNA polymerase sigma 55.4 14 0.0003 30.9 3.4 47 235-289 107-153 (160)
53 PRK09644 RNA polymerase sigma 55.4 14 0.0003 31.3 3.4 48 234-289 108-155 (165)
54 PF13443 HTH_26: Cro/C1-type H 55.4 10 0.00022 27.0 2.2 24 260-283 12-35 (63)
55 PRK11924 RNA polymerase sigma 54.9 13 0.00028 31.1 3.2 47 235-289 126-172 (179)
56 PF13518 HTH_28: Helix-turn-he 54.6 15 0.00032 24.9 2.9 24 261-284 15-38 (52)
57 PRK03975 tfx putative transcri 53.0 17 0.00036 31.5 3.5 49 232-289 4-52 (141)
58 PRK12514 RNA polymerase sigma 52.6 15 0.00032 31.5 3.2 47 235-289 130-176 (179)
59 TIGR02939 RpoE_Sigma70 RNA pol 52.2 12 0.00026 32.0 2.6 48 235-290 139-186 (190)
60 PRK09646 RNA polymerase sigma 52.0 15 0.00033 32.0 3.2 48 235-290 143-190 (194)
61 PF13730 HTH_36: Helix-turn-he 51.5 49 0.0011 22.9 5.2 47 235-284 3-51 (55)
62 PRK09652 RNA polymerase sigma 50.5 17 0.00037 30.5 3.2 47 235-289 129-175 (182)
63 TIGR02985 Sig70_bacteroi1 RNA 49.3 20 0.00043 29.4 3.3 47 234-288 113-159 (161)
64 TIGR02989 Sig-70_gvs1 RNA poly 48.8 21 0.00046 29.5 3.5 46 235-288 112-157 (159)
65 PRK06811 RNA polymerase factor 48.7 20 0.00044 31.1 3.4 48 234-289 131-178 (189)
66 PRK12526 RNA polymerase sigma 47.8 19 0.00041 31.9 3.2 47 235-289 154-200 (206)
67 PRK12541 RNA polymerase sigma 46.8 21 0.00045 30.0 3.1 47 234-288 112-158 (161)
68 TIGR02999 Sig-70_X6 RNA polyme 46.5 25 0.00053 30.0 3.6 47 235-289 135-181 (183)
69 PRK12512 RNA polymerase sigma 46.2 22 0.00049 30.4 3.3 49 234-290 131-179 (184)
70 PRK12547 RNA polymerase sigma 46.2 21 0.00046 30.2 3.1 47 235-289 113-159 (164)
71 PRK05602 RNA polymerase sigma 44.8 22 0.00049 30.6 3.1 49 235-291 129-177 (186)
72 PF13936 HTH_38: Helix-turn-he 44.6 25 0.00055 23.9 2.7 39 234-280 4-42 (44)
73 PRK12523 RNA polymerase sigma 44.2 25 0.00055 29.9 3.3 47 235-289 120-166 (172)
74 TIGR02983 SigE-fam_strep RNA p 43.8 26 0.00056 29.3 3.2 49 234-290 110-158 (162)
75 PRK09639 RNA polymerase sigma 43.4 26 0.00056 29.3 3.2 46 235-289 113-158 (166)
76 PRK09648 RNA polymerase sigma 43.1 27 0.00059 30.1 3.4 47 235-289 140-186 (189)
77 PF10668 Phage_terminase: Phag 42.9 21 0.00046 26.6 2.2 21 259-279 23-43 (60)
78 PRK12537 RNA polymerase sigma 41.7 29 0.00062 29.9 3.3 46 235-288 134-179 (182)
79 PRK12546 RNA polymerase sigma 41.6 25 0.00055 30.9 3.0 48 234-289 113-160 (188)
80 PRK12519 RNA polymerase sigma 40.9 22 0.00049 30.7 2.5 47 234-288 141-187 (194)
81 PF14086 DUF4266: Domain of un 40.8 17 0.00036 26.2 1.4 14 7-20 35-48 (50)
82 PRK12524 RNA polymerase sigma 40.7 28 0.0006 30.4 3.1 49 234-290 136-184 (196)
83 PRK12536 RNA polymerase sigma 40.2 32 0.0007 29.5 3.4 47 235-289 130-176 (181)
84 PRK12530 RNA polymerase sigma 39.6 31 0.00067 30.1 3.2 47 235-289 135-181 (189)
85 PRK09047 RNA polymerase factor 39.6 36 0.00077 28.2 3.5 47 235-289 107-153 (161)
86 PRK12531 RNA polymerase sigma 39.3 30 0.00066 30.1 3.1 51 234-292 141-191 (194)
87 PRK13919 putative RNA polymera 39.2 34 0.00073 29.3 3.3 47 235-289 136-182 (186)
88 PF01381 HTH_3: Helix-turn-hel 39.1 24 0.00053 24.2 2.0 21 261-281 12-32 (55)
89 PRK09413 IS2 repressor TnpA; R 39.0 52 0.0011 27.0 4.3 47 231-284 9-55 (121)
90 TIGR02948 SigW_bacill RNA poly 38.9 30 0.00064 29.5 2.9 47 235-289 137-183 (187)
91 PRK12515 RNA polymerase sigma 38.6 35 0.00076 29.5 3.4 47 235-289 132-178 (189)
92 TIGR02959 SigZ RNA polymerase 38.5 35 0.00077 29.1 3.3 47 235-289 101-147 (170)
93 KOG4445 Uncharacterized conser 38.1 72 0.0016 31.4 5.5 46 103-150 134-179 (368)
94 PRK12516 RNA polymerase sigma 37.9 33 0.00071 30.0 3.1 48 235-290 117-164 (187)
95 PF13384 HTH_23: Homeodomain-l 37.4 30 0.00065 23.4 2.2 23 261-283 20-42 (50)
96 cd00131 PAX Paired Box domain 37.1 93 0.002 26.0 5.6 45 235-282 76-127 (128)
97 PF04967 HTH_10: HTH DNA bindi 37.1 75 0.0016 23.0 4.3 47 235-282 1-47 (53)
98 PRK12532 RNA polymerase sigma 37.0 37 0.00079 29.5 3.2 47 235-289 137-183 (195)
99 PRK09636 RNA polymerase sigma 36.8 48 0.001 31.1 4.2 50 235-292 116-165 (293)
100 PRK09649 RNA polymerase sigma 36.8 39 0.00085 29.3 3.4 48 234-289 130-177 (185)
101 PRK12542 RNA polymerase sigma 36.5 37 0.0008 29.2 3.1 48 235-290 123-170 (185)
102 PRK15369 two component system 36.3 80 0.0017 25.9 5.1 48 234-290 149-196 (211)
103 PRK04217 hypothetical protein; 35.9 46 0.001 27.6 3.5 49 233-289 41-89 (110)
104 TIGR02954 Sig70_famx3 RNA poly 35.8 41 0.00088 28.4 3.3 47 235-289 120-166 (169)
105 PRK12520 RNA polymerase sigma 35.5 42 0.0009 29.1 3.4 47 235-289 132-178 (191)
106 cd01392 HTH_LacI Helix-turn-he 35.2 22 0.00048 24.2 1.3 21 263-283 2-22 (52)
107 TIGR03070 couple_hipB transcri 34.9 28 0.00061 23.6 1.8 23 261-283 18-40 (58)
108 PF15500 Toxin_39: Putative RN 34.7 94 0.002 25.1 4.8 37 100-143 45-81 (96)
109 PRK06986 fliA flagellar biosyn 34.7 36 0.00078 30.8 2.9 47 235-289 185-231 (236)
110 PRK09645 RNA polymerase sigma 34.6 42 0.0009 28.4 3.1 48 235-290 119-166 (173)
111 PRK12535 RNA polymerase sigma 34.5 44 0.00094 29.5 3.3 51 235-293 134-184 (196)
112 PRK09637 RNA polymerase sigma 34.5 40 0.00086 29.3 3.0 47 235-289 107-153 (181)
113 PRK11511 DNA-binding transcrip 34.3 51 0.0011 27.2 3.5 40 239-282 10-49 (127)
114 PRK07037 extracytoplasmic-func 34.0 46 0.00099 27.8 3.2 47 235-289 110-156 (163)
115 KOG4460 Nuclear pore complex, 34.0 78 0.0017 33.6 5.4 38 106-150 569-606 (741)
116 TIGR02943 Sig70_famx1 RNA poly 33.9 45 0.00099 29.0 3.3 48 234-289 131-178 (188)
117 PRK12543 RNA polymerase sigma 33.8 47 0.001 28.5 3.4 47 235-289 118-164 (179)
118 TIGR02980 SigBFG RNA polymeras 33.7 46 0.00099 29.8 3.4 47 234-288 178-224 (227)
119 PRK10072 putative transcriptio 33.6 29 0.00063 28.0 1.9 23 261-283 49-71 (96)
120 PF13411 MerR_1: MerR HTH fami 33.2 34 0.00074 24.6 2.1 18 262-279 4-21 (69)
121 PF12022 DUF3510: Domain of un 33.2 2.4E+02 0.0053 23.5 7.5 19 132-150 80-98 (125)
122 PRK12538 RNA polymerase sigma 32.7 38 0.00082 31.0 2.7 47 235-289 172-218 (233)
123 PF05190 MutS_IV: MutS family 32.7 77 0.0017 23.8 4.1 25 100-124 1-25 (92)
124 PRK12528 RNA polymerase sigma 32.5 53 0.0012 27.4 3.4 45 235-287 114-158 (161)
125 TIGR02957 SigX4 RNA polymerase 32.3 63 0.0014 30.2 4.2 50 235-292 109-158 (281)
126 PF13097 CENP-U: CENP-A nucleo 32.3 1.4E+02 0.0031 26.8 6.2 47 101-150 102-149 (175)
127 PRK08583 RNA polymerase sigma 32.3 54 0.0012 30.0 3.7 47 235-289 206-252 (257)
128 PRK12513 RNA polymerase sigma 32.2 22 0.00047 30.9 1.0 47 235-289 140-186 (194)
129 cd00093 HTH_XRE Helix-turn-hel 32.2 40 0.00086 21.5 2.1 21 262-282 16-36 (58)
130 PF02796 HTH_7: Helix-turn-hel 32.1 1E+02 0.0022 20.9 4.1 40 232-279 3-42 (45)
131 PRK12533 RNA polymerase sigma 31.7 46 0.001 30.1 3.1 48 234-289 134-181 (216)
132 PF07425 Pardaxin: Pardaxin; 31.5 30 0.00065 22.3 1.2 22 36-57 5-26 (33)
133 PRK09641 RNA polymerase sigma 31.4 49 0.0011 28.1 3.1 47 235-289 137-183 (187)
134 PF00196 GerE: Bacterial regul 31.3 78 0.0017 22.3 3.6 47 235-290 4-50 (58)
135 smart00421 HTH_LUXR helix_turn 31.3 70 0.0015 21.2 3.3 47 234-289 3-49 (58)
136 TIGR03001 Sig-70_gmx1 RNA poly 31.3 48 0.001 30.7 3.1 47 235-289 162-208 (244)
137 PRK09415 RNA polymerase factor 31.3 45 0.00098 28.6 2.9 47 234-288 127-173 (179)
138 PRK12539 RNA polymerase sigma 31.0 56 0.0012 28.1 3.4 47 235-289 132-178 (184)
139 TIGR02947 SigH_actino RNA poly 31.0 26 0.00055 30.5 1.2 47 235-289 132-178 (193)
140 PRK09647 RNA polymerase sigma 30.6 53 0.0011 29.2 3.2 47 235-289 139-185 (203)
141 PRK12544 RNA polymerase sigma 30.5 56 0.0012 29.2 3.4 48 234-289 148-195 (206)
142 PRK12522 RNA polymerase sigma 30.4 55 0.0012 27.8 3.2 47 235-289 120-166 (173)
143 PRK12529 RNA polymerase sigma 30.2 68 0.0015 27.5 3.8 47 235-289 128-174 (178)
144 PRK08301 sporulation sigma fac 29.8 52 0.0011 29.6 3.1 51 235-289 179-229 (234)
145 cd04761 HTH_MerR-SF Helix-Turn 29.7 51 0.0011 21.9 2.3 20 262-281 4-23 (49)
146 PRK08241 RNA polymerase factor 29.4 57 0.0012 31.1 3.4 49 235-291 154-202 (339)
147 PF12362 DUF3646: DNA polymera 29.4 25 0.00054 29.4 0.9 22 32-53 87-108 (117)
148 PF13551 HTH_29: Winged helix- 29.2 2E+02 0.0044 22.0 6.1 46 235-280 58-109 (112)
149 TIGR02941 Sigma_B RNA polymera 29.0 53 0.0012 30.1 3.1 48 234-289 205-252 (255)
150 TIGR02479 FliA_WhiG RNA polyme 29.0 58 0.0013 29.1 3.2 46 235-288 176-221 (224)
151 PRK07670 RNA polymerase sigma 28.7 59 0.0013 29.8 3.3 46 235-288 202-247 (251)
152 PRK12540 RNA polymerase sigma 28.6 57 0.0012 28.4 3.0 49 235-291 112-160 (182)
153 PRK12511 RNA polymerase sigma 28.6 59 0.0013 28.3 3.1 49 234-290 111-159 (182)
154 PF13865 FoP_duplication: C-te 28.5 56 0.0012 25.0 2.6 6 104-109 48-53 (74)
155 PRK12534 RNA polymerase sigma 28.0 61 0.0013 27.8 3.1 46 235-288 138-183 (187)
156 PF11288 DUF3089: Protein of u 27.9 20 0.00043 33.0 -0.0 28 33-64 110-137 (207)
157 PRK12527 RNA polymerase sigma 27.9 67 0.0015 26.7 3.3 47 235-289 106-152 (159)
158 PRK05657 RNA polymerase sigma 27.9 59 0.0013 31.5 3.3 53 234-290 262-314 (325)
159 PRK09635 sigI RNA polymerase s 27.8 73 0.0016 30.2 3.8 50 235-292 119-168 (290)
160 PF13613 HTH_Tnp_4: Helix-turn 27.8 1.2E+02 0.0025 21.3 4.0 41 235-282 3-43 (53)
161 smart00530 HTH_XRE Helix-turn- 27.7 50 0.0011 20.8 2.0 22 261-282 13-34 (56)
162 PRK06288 RNA polymerase sigma 27.3 61 0.0013 30.0 3.2 47 235-289 213-259 (268)
163 PRK11923 algU RNA polymerase s 27.3 61 0.0013 27.9 3.0 47 235-289 139-185 (193)
164 PRK12545 RNA polymerase sigma 27.2 66 0.0014 28.3 3.2 47 235-289 140-186 (201)
165 PHA01976 helix-turn-helix prot 26.8 48 0.001 23.7 1.9 22 261-282 18-39 (67)
166 TIGR02885 spore_sigF RNA polym 26.7 72 0.0016 28.6 3.5 47 234-288 183-229 (231)
167 PF00376 MerR: MerR family reg 26.3 57 0.0012 21.7 2.0 19 262-280 3-21 (38)
168 PF07037 DUF1323: Putative tra 26.2 69 0.0015 27.2 2.9 30 261-293 3-32 (122)
169 TIGR02952 Sig70_famx2 RNA poly 26.0 79 0.0017 26.3 3.4 47 234-288 122-168 (170)
170 PRK09651 RNA polymerase sigma 25.9 56 0.0012 27.8 2.5 45 235-287 120-164 (172)
171 TIGR02607 antidote_HigA addict 25.9 49 0.0011 24.3 1.9 23 261-283 21-43 (78)
172 PRK06930 positive control sigm 25.8 75 0.0016 28.0 3.3 48 234-289 114-161 (170)
173 PRK04053 rps13p 30S ribosomal 25.5 50 0.0011 28.9 2.1 29 228-256 49-77 (149)
174 PF05821 NDUF_B8: NADH-ubiquin 25.4 65 0.0014 29.0 2.8 22 254-275 35-57 (179)
175 TIGR02960 SigX5 RNA polymerase 25.3 78 0.0017 29.7 3.5 49 235-291 143-191 (324)
176 KOG4040 NADH:ubiquinone oxidor 25.3 54 0.0012 29.3 2.2 40 235-274 21-61 (186)
177 PRK12525 RNA polymerase sigma 25.2 90 0.002 26.4 3.6 46 234-287 118-163 (168)
178 TIGR02394 rpoS_proteo RNA poly 24.9 72 0.0016 29.9 3.2 52 234-289 222-273 (285)
179 PRK08295 RNA polymerase factor 24.4 78 0.0017 27.5 3.2 45 235-288 156-200 (208)
180 cd04762 HTH_MerR-trunc Helix-T 24.1 78 0.0017 20.4 2.4 22 262-283 4-25 (49)
181 PF14229 DUF4332: Domain of un 24.0 78 0.0017 26.3 2.9 27 255-281 26-52 (122)
182 KOG3755 SATB1 matrix attachmen 23.7 67 0.0015 34.3 2.9 58 228-287 647-707 (769)
183 PF06056 Terminase_5: Putative 23.5 70 0.0015 23.4 2.2 19 262-280 17-35 (58)
184 cd04764 HTH_MlrA-like_sg1 Heli 23.3 66 0.0014 23.2 2.1 20 262-281 4-23 (67)
185 PRK09640 RNA polymerase sigma 23.3 46 0.001 28.8 1.4 47 235-289 135-181 (188)
186 PRK07408 RNA polymerase sigma 23.2 85 0.0018 29.0 3.3 48 234-289 203-250 (256)
187 PF12844 HTH_19: Helix-turn-he 22.5 63 0.0014 22.9 1.8 23 261-283 15-37 (64)
188 PRK11922 RNA polymerase sigma 22.4 48 0.001 29.9 1.4 47 235-289 150-196 (231)
189 PRK12517 RNA polymerase sigma 22.3 98 0.0021 26.9 3.4 48 235-290 129-176 (188)
190 TIGR02393 RpoD_Cterm RNA polym 22.3 93 0.002 28.2 3.3 52 235-290 177-228 (238)
191 TIGR02859 spore_sigH RNA polym 22.2 1.1E+02 0.0025 26.2 3.7 28 261-288 168-195 (198)
192 TIGR02950 SigM_subfam RNA poly 22.1 79 0.0017 25.9 2.6 46 235-288 106-151 (154)
193 PF07042 TrfA: TrfA protein; 22.1 1.2E+02 0.0025 29.3 4.0 48 234-284 210-257 (282)
194 cd06170 LuxR_C_like C-terminal 22.0 1.3E+02 0.0029 19.9 3.3 30 260-289 17-46 (57)
195 cd01104 HTH_MlrA-CarA Helix-Tu 21.9 77 0.0017 22.6 2.2 19 262-280 4-22 (68)
196 PF02290 SRP14: Signal recogni 21.9 66 0.0014 25.7 2.0 19 100-118 70-88 (93)
197 PRK12518 RNA polymerase sigma 21.8 77 0.0017 26.7 2.5 48 235-290 121-168 (175)
198 PRK05803 sporulation sigma fac 21.7 81 0.0018 28.5 2.8 52 234-289 175-226 (233)
199 TIGR00721 tfx DNA-binding prot 21.3 1.2E+02 0.0026 26.1 3.6 48 232-288 4-51 (137)
200 PRK05572 sporulation sigma fac 20.8 99 0.0022 28.3 3.2 48 234-289 202-249 (252)
201 PF12323 HTH_OrfB_IS605: Helix 20.7 93 0.002 21.1 2.3 34 255-289 10-43 (46)
202 PF10281 Ish1: Putative stress 20.6 1.3E+02 0.0028 19.8 2.9 27 238-265 4-31 (38)
203 TIGR03826 YvyF flagellar opero 20.4 1.3E+02 0.0029 25.9 3.6 30 259-288 47-76 (137)
204 KOG4511 Uncharacterized conser 20.4 1.3E+02 0.0028 29.3 3.8 27 39-65 50-78 (335)
205 PF13551 HTH_29: Winged helix- 20.4 1E+02 0.0023 23.8 2.8 27 260-286 14-40 (112)
206 TIGR03629 arch_S13P archaeal r 20.1 82 0.0018 27.3 2.3 30 227-257 44-73 (144)
No 1
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=100.00 E-value=5.1e-36 Score=275.13 Aligned_cols=215 Identities=21% Similarity=0.372 Sum_probs=193.7
Q ss_pred hhHHHHHHHHHhCCChHHHHHHHHhh-----hcccCCCcccccHHHHHHHHHHHHHhhhccccccCCC-CCCCCCCCchH
Q 022056 31 ATVQLIKAEIASHPLYEQLLAAHVSC-----LRVATPIDQLPLIDAQLAQSHHVLRSYGSLQQANNNN-NHSLSPHERQE 104 (303)
Q Consensus 31 ~~~~~iKa~I~sHPlYp~Ll~A~i~C-----~KVgaP~e~~~~ld~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~dpE 104 (303)
++.++.|.+|.+||+||+|++++|+. +.|....|.-+. |+++.++++|+.+++++||+.++. ++..++|+..+
T Consensus 26 Deaqa~K~~lnch~mk~AlfsVLcE~KeKt~lsir~~qdeep~-dpqlmRLDnML~AEGVagPekgga~~~~Asgg~hsd 104 (334)
T KOG0774|consen 26 DEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRGMQDEEPP-DPQLMRLDNMLLAEGVAGPEKGGARAAAASGGDHSD 104 (334)
T ss_pred chHHhhhhccccccchHHHHHHHHHhhhhheeeeccccccCCC-ChHHHHHHHHHHHhcccCccccchhhhhccCCChHH
Confidence 34678999999999999999999995 667777766554 789999999999999999987665 55677788999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhHhhcHHHHHHhHHHHHHHHHHhhCCCCCCCCCCCCCcchhhhccCcCcCCCCCCcccc
Q 022056 105 LDNFLAQYLIVLCTFKEQLQQHVRVHAVEAVMGCREIENTLQALTGVSLGEGTGATMSDDEDDLHMDFSLDQSASDSHDL 184 (303)
Q Consensus 105 LDqFMeaYc~vL~kykeEL~kp~~~~~~EA~~f~~~ie~qL~~l~~~s~~~~~~~~~s~~e~~~~~d~~~~~~~~d~~d~ 184 (303)
+++.+.+ +++.|++||++ ...+|+++.+.+.+|+. +.
T Consensus 105 YR~kL~q---iR~iy~~Elek--------yeqaCneftthV~nlL~--------------------------------eQ 141 (334)
T KOG0774|consen 105 YRAKLLQ---IRQIYHNELEK--------YEQACNEFTTHVMNLLR--------------------------------EQ 141 (334)
T ss_pred HHHHHHH---HHHHHHHHHHH--------HHHHHHHHHHHHHHHHH--------------------------------Hh
Confidence 9998877 99999999987 67889999999999985 23
Q ss_pred ccCCCCCchhhhhhh--HHHHHHHHHHHHHHHHHHHHHHHHHHHH-hhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHH
Q 022056 185 MGFGPLLPTETERSL--MERVRQELKIELKQGFKSRIEDVREEIL-RKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDK 261 (303)
Q Consensus 185 ~~~~p~~~~~~e~~~--~~~~~~eLk~~l~~~y~~~~~~lr~e~~-kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek 261 (303)
+.++||.+.++|++. |.+.|..++..|++..|..+..||.+++ .+|||++|+|.++.+|..||..|..|||||++.|
T Consensus 142 sr~RPi~~ke~e~m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K 221 (334)
T KOG0774|consen 142 SRTRPIMPKEIERMVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAK 221 (334)
T ss_pred cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHH
Confidence 468999999999864 8999999999999999999999999998 5778899999999999999999999999999999
Q ss_pred HHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 262 AKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 262 ~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
+.||++|+++..||+|||.|+|.|.||.
T Consensus 222 ~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 222 EELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHHHHcCceehhhccccccceeehhhh
Confidence 9999999999999999999999999985
No 2
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.94 E-value=7.3e-29 Score=237.79 Aligned_cols=249 Identities=22% Similarity=0.277 Sum_probs=169.3
Q ss_pred HHHHHHHHHhCCChHHHHHHHHhhhcccCCCcccccHHHHHHHHHHHHHhhhccccccCCCCCCCCCCCchHHHHHHHHH
Q 022056 33 VQLIKAEIASHPLYEQLLAAHVSCLRVATPIDQLPLIDAQLAQSHHVLRSYGSLQQANNNNNHSLSPHERQELDNFLAQY 112 (303)
Q Consensus 33 ~~~iKa~I~sHPlYp~Ll~A~i~C~KVgaP~e~~~~ld~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dpELDqFMeaY 112 (303)
...+|..+.+||+|..++.||+.|+++++|.+.+.++++...........+..+... +....++...++++.||..|
T Consensus 49 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~---s~~~~~~~~~~~~~~~~~k~ 125 (342)
T KOG0773|consen 49 LASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRE---SATLKAWLEEHRLNPYPSKL 125 (342)
T ss_pred cccccccccchhHHhHHhhccccccccccCcCccccccccccCcccccccccccccc---ccccccchhhhhhccCchHH
Confidence 344799999999999999999999999999998887654322222111111111110 01223567899999999999
Q ss_pred HHHHHHHHHHHhhhHhhcHHHHHHhHHHHHHHHHHhhCCCCCCCCCCCCCcchhhhc----cCcCcCCCCCCccccccCC
Q 022056 113 LIVLCTFKEQLQQHVRVHAVEAVMGCREIENTLQALTGVSLGEGTGATMSDDEDDLH----MDFSLDQSASDSHDLMGFG 188 (303)
Q Consensus 113 c~vL~kykeEL~kp~~~~~~EA~~f~~~ie~qL~~l~~~s~~~~~~~~~s~~e~~~~----~d~~~~~~~~d~~d~~~~~ 188 (303)
+.+|..+...|+..+.+ ++++.++++++..+...+...+....+.+...+.++.. .+....+ +..++.
T Consensus 126 ~~~ll~~~~~~~~~~~~--~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~------~~~~~~ 197 (342)
T KOG0773|consen 126 EKILLAVITKLTLTQVS--TWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSE------ELLGES 197 (342)
T ss_pred HHHHHHHHHHhhhhhHH--HHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcccccccccccc------cccccc
Confidence 99999999999987522 79999999999999999875554333322221111110 0110000 000111
Q ss_pred CCCchhhhhhh--HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHH
Q 022056 189 PLLPTETERSL--MERVRQELKIELKQGFKSRIEDVREEILRKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVE 266 (303)
Q Consensus 189 p~~~~~~e~~~--~~~~~~eLk~~l~~~y~~~~~~lr~e~~kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~ 266 (303)
+....+.+... .......++..+.+.+..++........++|+++.||+.++.+|+.||.+|+.||||++.+|..||+
T Consensus 198 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~ 277 (342)
T KOG0773|consen 198 EQDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAK 277 (342)
T ss_pred cccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccch
Confidence 10000000000 0122344455555555555555555677889999999999999999999999999999999999999
Q ss_pred HhCCChHHHhhhhHhhhhhccccCCC
Q 022056 267 ETGLQLKQINNWFINQRKRNWHSNSQ 292 (303)
Q Consensus 267 ~tgLs~kQI~nWF~N~R~R~kk~~~~ 292 (303)
+|||+..||+|||||+|+|.|+|...
T Consensus 278 ~TGLs~~Qv~NWFINaR~R~w~p~~~ 303 (342)
T KOG0773|consen 278 QTGLSRPQVSNWFINARVRLWKPMIE 303 (342)
T ss_pred hcCCCcccCCchhhhcccccCCchHH
Confidence 99999999999999999999999663
No 3
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.89 E-value=1.9e-23 Score=150.08 Aligned_cols=50 Identities=44% Similarity=0.618 Sum_probs=46.9
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHHHHHhhhHhhcHHHHHHhHHHHHHHHHHhhC
Q 022056 97 LSPHERQELDNFLAQYLIVLCTFKEQLQQHVRVHAVEAVMGCREIENTLQALTG 150 (303)
Q Consensus 97 ~~~~~dpELDqFMeaYc~vL~kykeEL~kp~~~~~~EA~~f~~~ie~qL~~l~~ 150 (303)
.++++||||||||++||.||++||+||++|+ +||++|||+||+||++||+
T Consensus 3 ~~~~~dpELDqFMeaYc~~L~kykeeL~~p~----~EA~~f~~~ie~qL~~Lt~ 52 (52)
T PF03791_consen 3 SSIGADPELDQFMEAYCDMLVKYKEELQRPF----QEAMEFCREIEQQLSSLTG 52 (52)
T ss_pred CCCCCCccHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHhC
Confidence 3568999999999999999999999999995 8999999999999999985
No 4
>PF03790 KNOX1: KNOX1 domain ; InterPro: IPR005540 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.82 E-value=4.4e-21 Score=133.65 Aligned_cols=43 Identities=49% Similarity=0.772 Sum_probs=39.9
Q ss_pred HHHHHHHHhCCChHHHHHHHHhhhcccCCCcccccHHHHHHHH
Q 022056 34 QLIKAEIASHPLYEQLLAAHVSCLRVATPIDQLPLIDAQLAQS 76 (303)
Q Consensus 34 ~~iKa~I~sHPlYp~Ll~A~i~C~KVgaP~e~~~~ld~~~~~~ 76 (303)
+.|||+|++||+||+||+|||+|+|||||||++++||++.++.
T Consensus 1 e~iKA~I~~HP~Y~~Ll~Ayi~C~KVGAP~e~~~~L~e~~~~~ 43 (45)
T PF03790_consen 1 EAIKAKIASHPLYPRLLAAYIDCQKVGAPPEVVARLDEILAES 43 (45)
T ss_pred ChHHHHHHcCCCcHHHHHHHHHHHhcCCCHHHHHHHHHHHHHh
Confidence 3699999999999999999999999999999999999987654
No 5
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.67 E-value=5.1e-17 Score=111.26 Aligned_cols=40 Identities=50% Similarity=1.029 Sum_probs=36.4
Q ss_pred HHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhh
Q 022056 246 WWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKR 285 (303)
Q Consensus 246 wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R 285 (303)
||..|..|||||.++|..||.+|||+.+||+|||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 8999999999999999999999999999999999999997
No 6
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=99.61 E-value=1.2e-14 Score=129.17 Aligned_cols=154 Identities=18% Similarity=0.284 Sum_probs=121.3
Q ss_pred HHHHHHHHHhCCChHHHHHHHHhh-----hcccCCCcccccHHHHHHHHHHHHHhhhccccccCCCCC-CCCCC---Cch
Q 022056 33 VQLIKAEIASHPLYEQLLAAHVSC-----LRVATPIDQLPLIDAQLAQSHHVLRSYGSLQQANNNNNH-SLSPH---ERQ 103 (303)
Q Consensus 33 ~~~iKa~I~sHPlYp~Ll~A~i~C-----~KVgaP~e~~~~ld~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~---~dp 103 (303)
.+++|.+|.+||+||+|++++|+. +++..+.+..+. |+++.++++|+.++++.+|+.++... .+... ..-
T Consensus 26 aqa~K~~l~~hr~k~ALfsVLcE~KEkt~LSir~~qee~p~-dpQl~RLDNML~AEGV~gPe~~~~~~~~~~~~~~~~~~ 104 (191)
T PF03792_consen 26 AQARKHALNCHRMKPALFSVLCEIKEKTVLSIRNIQEEDPP-DPQLMRLDNMLLAEGVAGPEKGGRAAAAAAGTAADNSI 104 (191)
T ss_pred HHHhchhhcCCCCchhhHHHHHHHHhhcCccccccCCcCCC-chhhhhhhcchhhhcCcCCCCcccchhhhhccCccccc
Confidence 588999999999999999999995 556666554433 78899999999999999997655421 22111 111
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhHhhcHHHHHHhHHHHHHHHHHhhCCCCCCCCCCCCCcchhhhccCcCcCCCCCCccc
Q 022056 104 ELDNFLAQYLIVLCTFKEQLQQHVRVHAVEAVMGCREIENTLQALTGVSLGEGTGATMSDDEDDLHMDFSLDQSASDSHD 183 (303)
Q Consensus 104 ELDqFMeaYc~vL~kykeEL~kp~~~~~~EA~~f~~~ie~qL~~l~~~s~~~~~~~~~s~~e~~~~~d~~~~~~~~d~~d 183 (303)
|-+.|-...-.+...|+.||++ ....|+++.+.+.+|.. +
T Consensus 105 d~~dYr~kL~~ir~~y~~el~k--------ye~ac~eF~~hV~~lLr--------------------------------e 144 (191)
T PF03792_consen 105 DHSDYRAKLSQIRQIYHSELEK--------YEQACNEFTEHVMNLLR--------------------------------E 144 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHHH--------HHHHhhhhHHHHHHHHH--------------------------------H
Confidence 2333444455599999999986 56899999999999985 2
Q ss_pred cccCCCCCchhhhhhh--HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022056 184 LMGFGPLLPTETERSL--MERVRQELKIELKQGFKSRIEDVREEIL 227 (303)
Q Consensus 184 ~~~~~p~~~~~~e~~~--~~~~~~eLk~~l~~~y~~~~~~lr~e~~ 227 (303)
.+.|+||++.++|+++ +.+.|+-+..+||+..|+.+..||.+|+
T Consensus 145 Qs~~RPIs~keiE~m~~~i~~Kf~~iq~qLKQstCEaVm~LRsRfl 190 (191)
T PF03792_consen 145 QSEFRPISPKEIERMVNIIHRKFSKIQMQLKQSTCEAVMILRSRFL 190 (191)
T ss_pred hcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3469999999999864 8999999999999999999999998764
No 7
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.54 E-value=1.3e-14 Score=104.25 Aligned_cols=57 Identities=26% Similarity=0.599 Sum_probs=53.4
Q ss_pred ccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 230 RRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 230 rkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
+++..+++++..+|+.||..| |||+..++..||.+|||+.+||.+||+|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~---~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKN---PYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhC---CCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 566789999999999999997 999999999999999999999999999999998764
No 8
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.50 E-value=3.3e-14 Score=101.60 Aligned_cols=55 Identities=25% Similarity=0.573 Sum_probs=51.3
Q ss_pred ccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcc
Q 022056 230 RRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNW 287 (303)
Q Consensus 230 rkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~k 287 (303)
+.++.|+.++..+|+.||..| |||+..++..||..+||+.+||.+||+|+|.|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~---~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKN---PYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhC---CCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 456779999999999999988 7999999999999999999999999999999864
No 9
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.50 E-value=2.3e-14 Score=103.36 Aligned_cols=57 Identities=32% Similarity=0.778 Sum_probs=53.7
Q ss_pred hccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 229 KRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 229 krkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
||++..|+.++..+|+.+|..+ |||+..++..||..+||+..||.+||+|+|.+.|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~---~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQEN---PYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHS---SSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHh---ccccccccccccccccccccccccCHHHhHHHhCc
Confidence 5677889999999999999987 89999999999999999999999999999999874
No 10
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.35 E-value=1.2e-12 Score=122.05 Aligned_cols=81 Identities=33% Similarity=0.657 Sum_probs=61.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH----hhccCCCCC--c--------------chHHHHHHHHHHcCCCCCCCHHHHHH
Q 022056 204 RQELKIELKQGFKSRIEDVREEIL----RKRRAGKLP--G--------------DTTSVLKNWWQQHSKWPYPTEDDKAK 263 (303)
Q Consensus 204 ~~eLk~~l~~~y~~~~~~lr~e~~----kkrkr~~lp--k--------------~~~~~L~~wf~~h~~~PYPs~~ek~~ 263 (303)
...|++.++.......+.+|-+.+ |-|-|+||| + ..+.+|++||..+ |||++++|..
T Consensus 132 h~~LQ~lWl~AhY~EAek~RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~---~YPsp~eKRe 208 (304)
T KOG0775|consen 132 HPKLQALWLKAHYKEAEKLRGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQN---PYPSPREKRE 208 (304)
T ss_pred hHHHHHHHHHHHHHHHHHhcCCcCCccccceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcC---CCCChHHHHH
Confidence 355666666554444555554433 333334444 2 4899999999976 9999999999
Q ss_pred HHHHhCCChHHHhhhhHhhhhhcc
Q 022056 264 LVEETGLQLKQINNWFINQRKRNW 287 (303)
Q Consensus 264 LA~~tgLs~kQI~nWF~N~R~R~k 287 (303)
||+.|||+..||.|||.|+|.|.+
T Consensus 209 LA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 209 LAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred HHHHhCCchhhhhhhhhhhhhhhh
Confidence 999999999999999999999998
No 11
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.00 E-value=3.5e-10 Score=83.48 Aligned_cols=53 Identities=19% Similarity=0.460 Sum_probs=50.1
Q ss_pred hhccCCCCCcchHHHHHHHHHHcCCCCC----CCHHHHHHHHHHhCCChHHHhhhhHhhh
Q 022056 228 RKRRAGKLPGDTTSVLKNWWQQHSKWPY----PTEDDKAKLVEETGLQLKQINNWFINQR 283 (303)
Q Consensus 228 kkrkr~~lpk~~~~~L~~wf~~h~~~PY----Ps~~ek~~LA~~tgLs~kQI~nWF~N~R 283 (303)
+||.|++|+.+|+..|+..|..+ +| |+..++..||..+||+..+|.+||+|-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~---~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKL---GWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHc---CCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 47889999999999999999998 79 9999999999999999999999999954
No 12
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.98 E-value=2.9e-10 Score=100.74 Aligned_cols=62 Identities=18% Similarity=0.318 Sum_probs=57.1
Q ss_pred HhhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCC
Q 022056 227 LRKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNS 291 (303)
Q Consensus 227 ~kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~ 291 (303)
+-||.|+.|+.++...|+..|..+ -|-.-.||..||..++|++.||.+||||+|.|+|+...
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~---~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~ 162 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGN---QYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQ 162 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcC---CeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHH
Confidence 347888999999999999999998 59999999999999999999999999999999998643
No 13
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.95 E-value=2.9e-10 Score=108.52 Aligned_cols=60 Identities=20% Similarity=0.334 Sum_probs=55.1
Q ss_pred hccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCC
Q 022056 229 KRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNS 291 (303)
Q Consensus 229 krkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~ 291 (303)
||||-.++|.|+..|+.-|.-|. |.|++-|.+|++.++||.+||.+||||+|+|.||-+.
T Consensus 236 RKKRcPYTK~QtlELEkEFlfN~---YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 236 RKKRCPYTKHQTLELEKEFLFNM---YITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred ccccCCchHHHHHHHHHHHHHHH---HHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 44556799999999999999995 9999999999999999999999999999999999763
No 14
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.92 E-value=6.2e-10 Score=104.27 Aligned_cols=63 Identities=22% Similarity=0.312 Sum_probs=57.9
Q ss_pred hhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCCCC
Q 022056 228 RKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNSQS 293 (303)
Q Consensus 228 kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~~~ 293 (303)
.||.|+.|+..|+..|+.-|.-| -|-+...|.+||..+.|++.||.+||||+|++.||.+...
T Consensus 159 ~kR~RtayT~~QllELEkEFhfN---~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHFN---KYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred CCCCCcccchhhhhhhhhhhccc---cccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence 68888999999999999999988 5999999999999999999999999999999999865433
No 15
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.89 E-value=1.2e-09 Score=101.69 Aligned_cols=59 Identities=32% Similarity=0.478 Sum_probs=56.4
Q ss_pred hhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 228 RKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 228 kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
-||.|+-|+.++.+.|+.-|.+|. |.++..|+.||.++||.+.||.+||||+|.+.||.
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enR---YlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENR---YLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhh---hHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 377889999999999999999996 99999999999999999999999999999999996
No 16
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.84 E-value=1.6e-09 Score=99.16 Aligned_cols=59 Identities=22% Similarity=0.329 Sum_probs=54.4
Q ss_pred hhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 228 RKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 228 kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.||.|+.++.-+.+.|+.-|+.. -|.--.||.+||..+||+.+||.+||||+|.++||.
T Consensus 122 ~RKPRTIYSS~QLqaL~rRFQkT---QYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl 180 (245)
T KOG0850|consen 122 VRKPRTIYSSLQLQALNRRFQQT---QYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKL 180 (245)
T ss_pred ccCCcccccHHHHHHHHHHHhhc---chhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHH
Confidence 35677889999999999999988 599999999999999999999999999999999985
No 17
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.82 E-value=1.5e-09 Score=103.66 Aligned_cols=60 Identities=18% Similarity=0.349 Sum_probs=55.2
Q ss_pred HhhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 227 LRKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 227 ~kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
+|||+|=-|++.|+-.|+.-|.+.+ |-|-.||+.||..++||.+||.+||||+|.|-|+.
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrqQR---YLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~ 211 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQQR---YLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQ 211 (307)
T ss_pred cccccccccchhHHHHHHHHHHhhh---ccccHhHHHHHHhcCCCchheeeeeecchhhhhhh
Confidence 3566667799999999999999997 99999999999999999999999999999998875
No 18
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.79 E-value=2.1e-09 Score=105.00 Aligned_cols=67 Identities=15% Similarity=0.395 Sum_probs=61.8
Q ss_pred HHHHHHhhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCC
Q 022056 222 VREEILRKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNS 291 (303)
Q Consensus 222 lr~e~~kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~ 291 (303)
+-..-+|||||+.+...++..|+..|..| |-||-+|.-.||++++|.+..|++||+|+|.+.|+.++
T Consensus 288 i~a~~RkRKKRTSie~~vr~aLE~~F~~n---pKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 288 IGAQSRKRKKRTSIEVNVRGALEKHFLKN---PKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred hhccccccccccceeHHHHHHHHHHHHhC---CCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 33344678889999999999999999998 99999999999999999999999999999999999988
No 19
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.79 E-value=2.5e-09 Score=97.29 Aligned_cols=60 Identities=18% Similarity=0.299 Sum_probs=56.3
Q ss_pred HhhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 227 LRKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 227 ~kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.|||.|+.|+..|+..|+.-|.... |-+..+|..||+++.|++.||.+||||+|.+.|+.
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~kr---YLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKR---YLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHh---hhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 4788899999999999999999996 99999999999999999999999999999997764
No 20
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.75 E-value=6.3e-09 Score=94.06 Aligned_cols=58 Identities=28% Similarity=0.441 Sum_probs=52.2
Q ss_pred hccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 229 KRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 229 krkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
++++.+|+.+++..|+.-|..|. |-.+..|..||++.||++.||.+||||+|.|.|..
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~---~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~k 108 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEK---KLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTK 108 (198)
T ss_pred ccccccccHHHHHHhHHhhcccc---ccChHHHHHHHHhhCCChhHHHHHHhhccccccch
Confidence 34555699999999999999985 89999999999999999999999999999997654
No 21
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.74 E-value=6.7e-09 Score=99.66 Aligned_cols=60 Identities=20% Similarity=0.389 Sum_probs=54.7
Q ss_pred HhhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 227 LRKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 227 ~kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
++||.|+.|+..++..|+.-|+.-+ |-+..+|..||...||+-.||.+||||+|+|.|+.
T Consensus 171 K~RksRTaFT~~Ql~~LEkrF~~QK---YLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq 230 (309)
T KOG0488|consen 171 KRRKSRTAFSDHQLFELEKRFEKQK---YLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQ 230 (309)
T ss_pred ccccchhhhhHHHHHHHHHHHHHhh---cccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHH
Confidence 3566778899999999999999886 99999999999999999999999999999997764
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.71 E-value=9.6e-09 Score=89.77 Aligned_cols=62 Identities=23% Similarity=0.391 Sum_probs=56.1
Q ss_pred hhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCCC
Q 022056 228 RKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNSQ 292 (303)
Q Consensus 228 kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~~ 292 (303)
.+++|.+.+..++.+|+..|..+ |||+..+|..|+..++|+++-|..||||+|.+.|+....
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i~---p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEIN---PYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcccceechHHHHHHHHHHhccC---CCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 35566678999999999999988 999999999999999999999999999999999887544
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.69 E-value=1.2e-08 Score=89.37 Aligned_cols=62 Identities=18% Similarity=0.373 Sum_probs=56.4
Q ss_pred HHHhhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 225 EILRKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 225 e~~kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.-.++|.|+.|+-.+...|++-|+.-. |-+..++.+||...+|+++||..||||+|+++||-
T Consensus 97 ~~~r~K~Rtvfs~~ql~~l~~rFe~Qr---YLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~ 158 (194)
T KOG0491|consen 97 HCRRRKARTVFSDPQLSGLEKRFERQR---YLSTPERQELANALSLSETQVKTWFQNRRMKHKKQ 158 (194)
T ss_pred HHHhhhhcccccCccccccHHHHhhhh---hcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 344667788999999999999999875 99999999999999999999999999999999984
No 24
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.66 E-value=9.1e-09 Score=93.14 Aligned_cols=67 Identities=15% Similarity=0.274 Sum_probs=61.9
Q ss_pred HHHHHHHHhhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 220 EDVREEILRKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 220 ~~lr~e~~kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
..||+....++.|+.|+..|...|+.-|.+. .|-+.+||.+++..+.|+..||.+||||+|.|.|+.
T Consensus 136 C~LrKhk~nRkPRtPFTtqQLlaLErkfrek---qYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 136 CTLRKHKPNRKPRTPFTTQQLLALERKFREK---QYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred chhcccCCCCCCCCCCCHHHHHHHHHHHhHh---hhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 4678888888999999999999999999998 599999999999999999999999999999998864
No 25
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.45 E-value=1.3e-07 Score=88.25 Aligned_cols=55 Identities=20% Similarity=0.338 Sum_probs=51.3
Q ss_pred CCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 232 AGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 232 r~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
|+.|+..+...|++-|.+. -||+.-.|+.||..|+|.+..|.+||||+|.+.+|.
T Consensus 145 RTiFT~~Qle~LEkaFkea---HYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKEA---HYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred cchhhHHHHHHHHHHHhhc---cCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 7899999999999999987 499999999999999999999999999999987764
No 26
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.43 E-value=1.5e-07 Score=85.93 Aligned_cols=59 Identities=19% Similarity=0.369 Sum_probs=54.6
Q ss_pred hhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 228 RKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 228 kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.+|.|+.|+..+..+|+.-|.+-. ||+...+++||.+.+|.+.+|.+||.|+|.+.++-
T Consensus 37 qRRERTtFtr~QlevLe~LF~kTq---YPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 37 QRRERTTFTRKQLEVLEALFAKTQ---YPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred cccccceecHHHHHHHHHHHHhhc---CccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 467789999999999999999884 99999999999999999999999999999987764
No 27
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.42 E-value=2.3e-07 Score=76.03 Aligned_cols=58 Identities=16% Similarity=0.319 Sum_probs=52.5
Q ss_pred hccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 229 KRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 229 krkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
+|=|+.|+..+...|+..|.+- .||+.=.|++||....|+...|++||||+|.+++|-
T Consensus 18 RRIRTTFTS~QLkELErvF~ET---HYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 18 RRIRTTFTSAQLKELERVFAET---HYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred hhhhhhhhHHHHHHHHHHHHhh---cCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 4456789999999999999886 499999999999999999999999999999999875
No 28
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.35 E-value=1.3e-07 Score=88.49 Aligned_cols=54 Identities=24% Similarity=0.390 Sum_probs=48.8
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
.++..++-.|+.-|..+ +|.|...|.+||..+||+++||.+||||+|.+.+|-|
T Consensus 205 VYTDhQRLELEKEfh~S---ryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 205 VYTDHQRLELEKEFHTS---RYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred Eecchhhhhhhhhhccc---cceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 46778999999988877 7999999999999999999999999999999988754
No 29
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.29 E-value=2.7e-07 Score=88.07 Aligned_cols=60 Identities=18% Similarity=0.381 Sum_probs=54.4
Q ss_pred hhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 228 RKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 228 kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
++|.|+-|+..+.+.|+.||.+|. ||+.+.|++||-.|+|+...|++||.|+|.+.+|..
T Consensus 112 qrrQrthFtSqqlqele~tF~rNr---ypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE 171 (351)
T KOG0486|consen 112 QRRQRTHFTSQQLQELEATFQRNR---YPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 171 (351)
T ss_pred hhhhhhhhHHHHHHHHHHHHhhcc---CCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence 345667799999999999999996 999999999999999999999999999999877753
No 30
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.10 E-value=1.4e-06 Score=82.47 Aligned_cols=71 Identities=21% Similarity=0.427 Sum_probs=61.0
Q ss_pred HHHHHHHhhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCCCCC
Q 022056 221 DVREEILRKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNSQSV 294 (303)
Q Consensus 221 ~lr~e~~kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~~~~ 294 (303)
.|..+...||.|+.++..+...|++.|... |-|-.--|++|+.+|||+-..|++||||+|.+.|+-.-.+.
T Consensus 160 ~l~gd~~nKRPRTTItAKqLETLK~AYn~S---pKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 160 ELEGDASNKRPRTTITAKQLETLKQAYNTS---PKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred ccccccccCCCcceeeHHHHHHHHHHhcCC---CchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence 344456689999999999999999988765 99999999999999999999999999999998877654443
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.06 E-value=4.2e-06 Score=84.92 Aligned_cols=56 Identities=18% Similarity=0.383 Sum_probs=53.0
Q ss_pred hhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhc
Q 022056 228 RKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRN 286 (303)
Q Consensus 228 kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~ 286 (303)
-||.|-.|+..+++.|...|.++ |||+.+.-+.|+.+++|....|.|||-|+|+|.
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke~---~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKEN---KRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhcC---CCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 47778889999999999999999 899999999999999999999999999999994
No 32
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=98.05 E-value=1.3e-06 Score=83.18 Aligned_cols=62 Identities=15% Similarity=0.253 Sum_probs=51.3
Q ss_pred CCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCCCCCch
Q 022056 232 AGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNSQSVTS 296 (303)
Q Consensus 232 r~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~~~~~~ 296 (303)
|+-|+.+|+..|+.-|++. -|-+...|.+||..++|.+..|.+||||+|++.|+-...-+|+
T Consensus 185 RTAFTReQIaRLEKEFyrE---NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWP 246 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYRE---NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWP 246 (408)
T ss_pred HhhhhHHHHHHHHHHHHHh---ccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCC
Confidence 4669999999996666544 2999999999999999999999999999999999865444443
No 33
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.98 E-value=3.8e-06 Score=76.99 Aligned_cols=63 Identities=24% Similarity=0.431 Sum_probs=54.7
Q ss_pred hhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCCCC
Q 022056 228 RKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNSQS 293 (303)
Q Consensus 228 kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~~~ 293 (303)
||..+..|+..++..|+.-|++.. ||--.++.+||...|++..||.+||||+|.+.+|.....
T Consensus 167 rk~srPTf~g~qi~~le~~feqtk---ylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaE 229 (288)
T KOG0847|consen 167 RKQSRPTFTGHQIYQLERKFEQTK---YLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAE 229 (288)
T ss_pred ccccCCCccchhhhhhhhhhhhhh---cccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccc
Confidence 444556689999999999999984 999999999999999999999999999999988765444
No 34
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.97 E-value=1.8e-06 Score=81.78 Aligned_cols=64 Identities=20% Similarity=0.454 Sum_probs=58.0
Q ss_pred hhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCCCCC
Q 022056 228 RKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNSQSV 294 (303)
Q Consensus 228 kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~~~~ 294 (303)
|||||+.+-..-++.|+.||... |-|+-+-...+|+++.|....|++||+|+|.+.|+-..+++
T Consensus 309 kKRKRTSIAAPEKRsLEayFavQ---PRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa~ 372 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAVQ---PRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSAT 372 (385)
T ss_pred cccccccccCcccccHHHHhccC---CCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhhc
Confidence 78899999888899999999988 99999999999999999999999999999999988655443
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.91 E-value=4.6e-06 Score=74.86 Aligned_cols=63 Identities=13% Similarity=0.147 Sum_probs=57.2
Q ss_pred HHHhhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 225 EILRKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 225 e~~kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
.+.+++.|..|+..+.+.|+.-|... +||+...++.||..+++++..|.+||+|+|.++++..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~---h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKV---HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCC---CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 34567788899999999999999988 7999999999999999999999999999999988754
No 36
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.86 E-value=1.1e-05 Score=78.87 Aligned_cols=60 Identities=25% Similarity=0.495 Sum_probs=54.4
Q ss_pred hccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCC
Q 022056 229 KRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNS 291 (303)
Q Consensus 229 krkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~ 291 (303)
+|.|+.|+..+...|..+|... |||....|+.||.+++|+...|+.||.|+|.+.++-.+
T Consensus 177 rr~rtsft~~Q~~~le~~f~rt---~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 177 RRNRTSFSPSQLEALEECFQRT---PYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccccchHHHHHHHhcCC---CCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 3446789999999999999988 79999999999999999999999999999998887653
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.50 E-value=6.2e-05 Score=72.60 Aligned_cols=64 Identities=31% Similarity=0.552 Sum_probs=59.1
Q ss_pred hccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCCCC
Q 022056 229 KRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNSQS 293 (303)
Q Consensus 229 krkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~~~ 293 (303)
.+++++++.+. ..|+.|...|..+|||++.++..|+-.++++..||++||+|.|+|.++.+..+
T Consensus 96 ~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~ 159 (342)
T KOG0773|consen 96 GARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMT 159 (342)
T ss_pred ccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCC
Confidence 45678899999 99999999999999999999999999999999999999999999999876554
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.49 E-value=9.5e-05 Score=54.27 Aligned_cols=43 Identities=19% Similarity=0.533 Sum_probs=31.8
Q ss_pred HHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhh
Q 022056 240 TSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKR 285 (303)
Q Consensus 240 ~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R 285 (303)
.+.|+++|..| .+..+.+-..|+.+|+|+..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~~h---~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKH---KQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT-------TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHc---CCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 45699999999 59999999999999999999999999877543
No 39
>PF03789 ELK: ELK domain ; InterPro: IPR005539 This domain is required for the nuclear localisation of these proteins []. All of these proteins are members of the Tale/Knox homeodomain family, a subfamily, containing homeobox IPR001356 from INTERPRO.; GO: 0003677 DNA binding, 0005634 nucleus
Probab=96.99 E-value=0.0006 Score=41.06 Aligned_cols=22 Identities=32% Similarity=0.483 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 022056 206 ELKIELKQGFKSRIEDVREEIL 227 (303)
Q Consensus 206 eLk~~l~~~y~~~~~~lr~e~~ 227 (303)
|||.+|+++|+++|.+||+||+
T Consensus 1 ELK~~LlrkY~g~i~~Lr~Ef~ 22 (22)
T PF03789_consen 1 ELKHQLLRKYSGYISSLRQEFS 22 (22)
T ss_pred CHHHHHHHHHhHhHHHHHHHhC
Confidence 5899999999999999999974
No 40
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=95.97 E-value=0.0054 Score=54.96 Aligned_cols=60 Identities=30% Similarity=0.545 Sum_probs=52.0
Q ss_pred hhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 228 RKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 228 kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
.++.+..+...+...|...|... |||....+..|+..+|++...|.+||+|.|.+.++..
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~---~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRAT---PKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred cCCCccccccchhHhhhhcccCC---CCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 34556677788888888888777 8999999999999999999999999999999998653
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=92.01 E-value=0.12 Score=58.07 Aligned_cols=60 Identities=22% Similarity=0.354 Sum_probs=53.2
Q ss_pred hhccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 228 RKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 228 kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
+++.|..+.-.+..+++..|..-. ||+.++-+.|.+..+|....|..||+|.|.+.+|..
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~---~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQR---TPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhcc---CChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 345566688888999999998885 999999999999999999999999999999999873
No 42
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=89.67 E-value=0.49 Score=33.99 Aligned_cols=47 Identities=15% Similarity=0.218 Sum_probs=32.3
Q ss_pred hccCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhh
Q 022056 229 KRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQR 283 (303)
Q Consensus 229 krkr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R 283 (303)
||+|..|+-+.+-.+-..+... + -...||+.+|++..+|++|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g-----~---s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEG-----E---SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCT-----T----HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcC-----C---CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 4566778877766665655544 3 578999999999999999999964
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=85.26 E-value=1.7 Score=46.72 Aligned_cols=48 Identities=23% Similarity=0.574 Sum_probs=44.1
Q ss_pred HHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 240 TSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 240 ~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
+.+|+.+|..| +.|+.++...+|.+-||...-|..||.+.+.....-+
T Consensus 568 ~sllkayyaln---~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALN---GLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhc---CCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 78899999988 8999999999999999999999999999998776654
No 44
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=79.25 E-value=3.2 Score=27.42 Aligned_cols=45 Identities=13% Similarity=0.150 Sum_probs=35.2
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNW 287 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~k 287 (303)
+|...+.++...+... ..-..+|+.+|++..+|..|....+.+.+
T Consensus 11 l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 11 LPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred CCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 6777888887776544 23457899999999999999988887653
No 45
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=78.43 E-value=3.1 Score=28.97 Aligned_cols=43 Identities=19% Similarity=0.258 Sum_probs=32.8
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhh
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKR 285 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R 285 (303)
||...+.++.-.|... -.-.++|+.+|++...|.+|....|++
T Consensus 11 L~~~~r~i~~l~~~~g--------~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG--------MSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC--------cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 8888888887776655 345689999999999999999998876
No 46
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=77.14 E-value=3.1 Score=30.78 Aligned_cols=45 Identities=11% Similarity=0.231 Sum_probs=30.3
Q ss_pred cCCCCCcchHHHHHHHH-HHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhh
Q 022056 231 RAGKLPGDTTSVLKNWW-QQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQR 283 (303)
Q Consensus 231 kr~~lpk~~~~~L~~wf-~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R 283 (303)
+++.||.+.+..+..-+ .. ......+|...|+++.+|.+|-.-.+
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~--------g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLES--------GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHHHHH--------HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHC--------CCceEeeecccccccccccHHHHHHh
Confidence 44568888866554443 33 36778999999999999999988776
No 47
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=77.05 E-value=3.2 Score=28.68 Aligned_cols=47 Identities=13% Similarity=0.193 Sum_probs=37.1
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
.||...+.+|...|... ..-.++|+..|++...|+.+......+.|+
T Consensus 4 ~L~~~er~vi~~~y~~~--------~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG--------LTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTST---------SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC--------CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 48888999998887544 235689999999999999999998888763
No 48
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=75.80 E-value=6 Score=23.27 Aligned_cols=39 Identities=10% Similarity=0.169 Sum_probs=27.5
Q ss_pred CCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhh
Q 022056 233 GKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWF 279 (303)
Q Consensus 233 ~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF 279 (303)
..++.+.+..+...+... + ....+|+.+|++...|.+|.
T Consensus 4 ~~~~~~~~~~i~~~~~~~----~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAAG----E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHhC
Confidence 346666666666665432 3 34578899999999999994
No 49
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=65.20 E-value=7.9 Score=32.08 Aligned_cols=47 Identities=9% Similarity=0.066 Sum_probs=38.7
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
.||+..++++...|.... .-.++|+.+|++...|.+|....|++.++
T Consensus 106 ~L~~~~r~ii~l~~~~~~--------s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGK--------TMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 388889999877666552 24589999999999999999999998875
No 50
>PRK00118 putative DNA-binding protein; Validated
Probab=58.86 E-value=12 Score=30.79 Aligned_cols=47 Identities=9% Similarity=0.087 Sum_probs=39.0
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||..+++++.-++.... .-..+|+.+|+++..|.+|+...|++.++-
T Consensus 18 L~ekqRevl~L~y~eg~--------S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY--------SLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 78888899988777662 234699999999999999999999888764
No 51
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=55.97 E-value=13 Score=29.51 Aligned_cols=46 Identities=17% Similarity=0.258 Sum_probs=35.8
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
||+..++++.-.+... + .-..+|+.+|+++..|.+|....+.+.++
T Consensus 111 L~~~~~~ii~~~~~~g----~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYLEG----L----SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 7777888875544433 3 33489999999999999999999988775
No 52
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=55.44 E-value=14 Score=30.90 Aligned_cols=47 Identities=13% Similarity=0.198 Sum_probs=39.2
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.+.... + -.++|+.+|++...|.+++..+|++.++.
T Consensus 107 Lp~~~r~v~~l~~~~g~----s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 107 LPENYRDVVLAHYLEEK----S----YQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred CCHHHHHHHHHHHHhCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 89999999977766663 2 24799999999999999999999988764
No 53
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=55.35 E-value=14 Score=31.25 Aligned_cols=48 Identities=15% Similarity=0.044 Sum_probs=40.4
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.||...++++.-++..++ .-.++|..+|++...|.+|..-.|++.++-
T Consensus 108 ~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 108 TLPVIEAQAILLCDVHEL--------TYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred hCCHHHHHHHHhHHHhcC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 388899999988777663 235899999999999999999999998864
No 54
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=55.35 E-value=10 Score=27.00 Aligned_cols=24 Identities=13% Similarity=0.275 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhh
Q 022056 260 DKAKLVEETGLQLKQINNWFINQR 283 (303)
Q Consensus 260 ek~~LA~~tgLs~kQI~nWF~N~R 283 (303)
....||+.+|+++.+|+.|+.+..
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 456899999999999999999773
No 55
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=54.91 E-value=13 Score=31.11 Aligned_cols=47 Identities=13% Similarity=0.155 Sum_probs=37.9
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||+..++++.-.+.... .-..+|+..|++...|.+|+.-.|++.++.
T Consensus 126 L~~~~r~i~~l~~~~~~--------~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 126 LPVKQREVFLLRYVEGL--------SYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CCHHHHHHhhHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 77788888876655542 236899999999999999999999998753
No 56
>PF13518 HTH_28: Helix-turn-helix domain
Probab=54.61 E-value=15 Score=24.91 Aligned_cols=24 Identities=17% Similarity=0.427 Sum_probs=21.0
Q ss_pred HHHHHHHhCCChHHHhhhhHhhhh
Q 022056 261 KAKLVEETGLQLKQINNWFINQRK 284 (303)
Q Consensus 261 k~~LA~~tgLs~kQI~nWF~N~R~ 284 (303)
...+|.+.|++..+|.+|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 446999999999999999988776
No 57
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=53.02 E-value=17 Score=31.51 Aligned_cols=49 Identities=10% Similarity=0.062 Sum_probs=38.6
Q ss_pred CCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 232 AGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 232 r~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
...||+.++++|.- +... -.-.++|+.+|++...|.+|..+.+++.++.
T Consensus 4 ~~~Lt~rqreVL~l-r~~G--------lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~ 52 (141)
T PRK03975 4 ESFLTERQIEVLRL-RERG--------LTQQEIADILGTSRANVSSIEKRARENIEKA 52 (141)
T ss_pred ccCCCHHHHHHHHH-HHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35688899999877 3333 2345899999999999999999999887753
No 58
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=52.62 E-value=15 Score=31.45 Aligned_cols=47 Identities=13% Similarity=0.256 Sum_probs=38.9
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.|.... + -..+|+.+|++...|.+++...|++.++-
T Consensus 130 L~~~~r~i~~l~~~~g~----s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 130 LEKDRAAAVRRAYLEGL----S----YKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CCHHHHHHHHHHHHcCC----C----HHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 78888888887776552 2 45799999999999999999999998764
No 59
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=52.23 E-value=12 Score=32.02 Aligned_cols=48 Identities=8% Similarity=0.007 Sum_probs=38.5
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
||...++++.-.|..+ -.-.++|+.+|++...|.++.-..|++.++..
T Consensus 139 L~~~~r~v~~l~~~~~--------~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 139 LPEDLRTAITLRELEG--------LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred CCHHHhhhhhhhhhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 7778888887655555 23458999999999999999999999988653
No 60
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=52.00 E-value=15 Score=32.00 Aligned_cols=48 Identities=8% Similarity=0.010 Sum_probs=40.1
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
||...+.+|.-.+..+. .-.++|+.+|++...|.+++...|++.++..
T Consensus 143 L~~~~r~vl~l~~~~~~--------s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 143 LTDTQRESVTLAYYGGL--------TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 89999999977766662 2357999999999999999999999988654
No 61
>PF13730 HTH_36: Helix-turn-helix domain
Probab=51.47 E-value=49 Score=22.86 Aligned_cols=47 Identities=11% Similarity=0.166 Sum_probs=30.5
Q ss_pred CCcchHHHHHHHHH--HcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhh
Q 022056 235 LPGDTTSVLKNWWQ--QHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRK 284 (303)
Q Consensus 235 lpk~~~~~L~~wf~--~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~ 284 (303)
|+..++.++..-+. .+..+.||| ...||+.+|++.+.|..++..-..
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~~~pS---~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGGCFPS---QETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCCCCcC---HHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45555555432222 123348887 557999999999999998876544
No 62
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=50.54 E-value=17 Score=30.51 Aligned_cols=47 Identities=11% Similarity=0.145 Sum_probs=37.9
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||+..++++.-.|... ++ -..+|+.+|++...|.+|....|++.++.
T Consensus 129 L~~~~r~vl~l~~~~~----~s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 129 LPEELRTAITLREIEG----LS----YEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred CCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 8888889987765555 22 24789999999999999999999998764
No 63
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=49.31 E-value=20 Score=29.36 Aligned_cols=47 Identities=17% Similarity=0.190 Sum_probs=37.1
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
.||...++++.-.+... ++ -..+|+.+|++...|.++....|++.++
T Consensus 113 ~L~~~~r~il~l~~~~~----~~----~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEG----KS----YKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 37888888887755544 22 3368999999999999999999998875
No 64
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=48.77 E-value=21 Score=29.54 Aligned_cols=46 Identities=20% Similarity=0.246 Sum_probs=37.7
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
||...++++.-.|... ++ -..+|+.+|++...|.++....|++.++
T Consensus 112 L~~~~r~v~~l~~~~g----~~----~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 112 LPERQRELLQLRYQRG----VS----LTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred CCHHHHHHHHHHHhcC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 8888999998866655 22 3478999999999999999999988765
No 65
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=48.71 E-value=20 Score=31.14 Aligned_cols=48 Identities=15% Similarity=0.178 Sum_probs=39.8
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
+||...+.++.-.|.... + -.++|+.+|++...|.+...-.|++.++.
T Consensus 131 ~L~~~~r~i~~l~~~~g~--s------~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 131 DLEKLDREIFIRRYLLGE--K------IEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred hCCHHHHHHHHHHHHccC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 489999999987666552 2 34799999999999999999999998875
No 66
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=47.83 E-value=19 Score=31.90 Aligned_cols=47 Identities=15% Similarity=0.191 Sum_probs=38.9
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.+...+ .-.++|+.+|++...|.+++...|++.++-
T Consensus 154 L~~~~r~vl~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 154 LPEAQQTVVKGVYFQEL--------SQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 88889999987666552 345899999999999999999999988754
No 67
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=46.77 E-value=21 Score=29.97 Aligned_cols=47 Identities=23% Similarity=0.154 Sum_probs=39.5
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
.||..++.++.-.+..+. + -.++|..+|++...|.++....|++.++
T Consensus 112 ~L~~~~r~v~~l~~~~~~----s----~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYYGF----S----YKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 489999999988777663 2 3478999999999999999999999875
No 68
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=46.47 E-value=25 Score=30.03 Aligned_cols=47 Identities=9% Similarity=0.058 Sum_probs=39.5
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||..++.++.-.+.... .-.++|+.+|++...|.+.+...|++.++.
T Consensus 135 Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFFAGL--------TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 89999999988777663 234799999999999999999999988753
No 69
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=46.18 E-value=22 Score=30.44 Aligned_cols=49 Identities=6% Similarity=-0.046 Sum_probs=40.6
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
.||...+.++.-.+.... .-.++|..+|++...|.+++...|++.++..
T Consensus 131 ~L~~~~r~v~~l~~~~g~--------s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEGA--------SIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 488889999988766552 2458999999999999999999999988653
No 70
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=46.17 E-value=21 Score=30.21 Aligned_cols=47 Identities=13% Similarity=0.022 Sum_probs=39.2
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...++++.-.+.... + -.++|+.+|+++..|.++..-.|++.++-
T Consensus 113 L~~~~r~v~~l~~~~g~----s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 113 LSADQREAIILIGASGF----S----YEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred CCHHHHHHHHHHHHcCC----C----HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 88889999888766663 2 34799999999999999999999998754
No 71
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=44.81 E-value=22 Score=30.57 Aligned_cols=49 Identities=8% Similarity=0.104 Sum_probs=39.2
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNS 291 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~ 291 (303)
||+..+.++.-.|.... .-.++|+.+|++...|.++....|++.++...
T Consensus 129 L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 129 LPERQREAIVLQYYQGL--------SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CCHHHHHHhhHHHhcCC--------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 78888888876655552 23479999999999999999999999987543
No 72
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=44.61 E-value=25 Score=23.94 Aligned_cols=39 Identities=8% Similarity=0.103 Sum_probs=21.8
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhH
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFI 280 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~ 280 (303)
.|+.+.+..+..++... .-...+|+..|.++..|.+|..
T Consensus 4 ~Lt~~eR~~I~~l~~~G--------~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 4 HLTPEERNQIEALLEQG--------MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp --------HHHHHHCS-----------HHHHHHHTT--HHHHHHHHH
T ss_pred chhhhHHHHHHHHHHcC--------CCHHHHHHHHCcCcHHHHHHHh
Confidence 48888888898887655 2345699999999999999864
No 73
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=44.24 E-value=25 Score=29.87 Aligned_cols=47 Identities=9% Similarity=0.209 Sum_probs=38.5
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||..++.++.-.+.... + -.++|+.+|++...|.++....+++.+..
T Consensus 120 Lp~~~r~v~~L~~~~g~--s------~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 120 LSSKARAAFLYNRLDGM--G------HAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CCHHHHHHHHHHHHcCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 88889899877666553 2 34799999999999999999999988654
No 74
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=43.83 E-value=26 Score=29.28 Aligned_cols=49 Identities=14% Similarity=0.226 Sum_probs=39.3
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
.||...+.++.-.|.... + -..+|..+|++...|.++....|++.++..
T Consensus 110 ~L~~~~r~i~~l~~~~g~----s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 110 RLPARQRAVVVLRYYEDL----S----EAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hCCHHHHHHhhhHHHhcC----C----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 388888899877666552 2 347899999999999999999999988753
No 75
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=43.36 E-value=26 Score=29.31 Aligned_cols=46 Identities=13% Similarity=0.229 Sum_probs=37.9
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||..++.+|.-.+ .. + .-..+|..+|++...|.++....|++.++-
T Consensus 113 L~~~~r~il~l~~-~g----~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 113 MTERDRTVLLLRF-SG----Y----SYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred CCHHHHHHHHHHH-cC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 7888888887776 55 2 345799999999999999999999988763
No 76
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=43.12 E-value=27 Score=30.10 Aligned_cols=47 Identities=13% Similarity=-0.019 Sum_probs=38.7
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.|.... .-.++|..+|++...|.++....|++.++.
T Consensus 140 L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 140 LPEKQREILILRVVVGL--------SAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 88888899887665552 245899999999999999999999988764
No 77
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=42.89 E-value=21 Score=26.59 Aligned_cols=21 Identities=19% Similarity=0.366 Sum_probs=17.9
Q ss_pred HHHHHHHHHhCCChHHHhhhh
Q 022056 259 DDKAKLVEETGLQLKQINNWF 279 (303)
Q Consensus 259 ~ek~~LA~~tgLs~kQI~nWF 279 (303)
-.-..||++.|++..||..|=
T Consensus 23 i~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 23 IKLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred ccHHHHHHHHCCCHHHHHHHh
Confidence 345689999999999999994
No 78
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=41.65 E-value=29 Score=29.91 Aligned_cols=46 Identities=13% Similarity=0.237 Sum_probs=37.5
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
||...+.++.--|.... .-..+|+.+|++...|.+|...+|++.++
T Consensus 134 L~~~~r~i~~l~~~~~~--------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 134 LEPARRNCILHAYVDGC--------SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 88888888777666552 24579999999999999999999998775
No 79
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=41.58 E-value=25 Score=30.86 Aligned_cols=48 Identities=15% Similarity=0.081 Sum_probs=39.9
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.||...++++.-.+.... + -.++|..+|++...|.+++.-.|++.++.
T Consensus 113 ~Lp~~~r~v~~L~~~~g~----s----~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~ 160 (188)
T PRK12546 113 QLPDEQREALILVGASGF----S----YEEAAEMCGVAVGTVKSRANRARARLAEL 160 (188)
T ss_pred hCCHHHhHHhhhHHhcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 389999999988766652 2 34789999999999999999999998875
No 80
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=40.93 E-value=22 Score=30.71 Aligned_cols=47 Identities=13% Similarity=0.188 Sum_probs=37.6
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
.||+..+.++.-.+.... .-.++|..+|++...|.+|+...|++.++
T Consensus 141 ~L~~~~~~v~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 141 QLPESQRQVLELAYYEGL--------SQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hCCHHHhhhhhhhhhcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 378888888866655442 23579999999999999999999998875
No 81
>PF14086 DUF4266: Domain of unknown function (DUF4266)
Probab=40.80 E-value=17 Score=26.25 Aligned_cols=14 Identities=43% Similarity=0.907 Sum_probs=8.3
Q ss_pred ccccCCCCCCCCCC
Q 022056 7 GVMGSSSSGGGGGG 20 (303)
Q Consensus 7 ~~~~~~~~~~~~~~ 20 (303)
|+.+|++.+||||+
T Consensus 35 ~a~gg~g~~GGGCG 48 (50)
T PF14086_consen 35 GASGGGGKAGGGCG 48 (50)
T ss_pred cccCCCCCCCcCCC
Confidence 44456666667665
No 82
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=40.72 E-value=28 Score=30.43 Aligned_cols=49 Identities=6% Similarity=0.047 Sum_probs=39.6
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
.||+..+.++.-.+... |+ -.++|+.+|++...|.+++.-+|++.++-.
T Consensus 136 ~L~~~~r~i~~L~~~~g----~s----~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIEG----LS----NPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 38888888887765555 23 347999999999999999999999988753
No 83
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=40.23 E-value=32 Score=29.54 Aligned_cols=47 Identities=15% Similarity=-0.001 Sum_probs=38.2
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||+..+.++.-.+..+. .-.++|+.+|++...|.+.+...|++.++.
T Consensus 130 L~~~~r~v~~l~~~~g~--------s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 130 LPDRQRLPIVHVKLEGL--------SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 78888888776666662 235799999999999999999999998863
No 84
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=39.64 E-value=31 Score=30.06 Aligned_cols=47 Identities=11% Similarity=0.121 Sum_probs=39.3
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.+.... .-.++|..+|+++..|.++..-+|++.++-
T Consensus 135 Lp~~~R~v~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 135 LPAQQARVFMMREYLEL--------SSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred CCHHHHHHHhHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 88889999987766652 245899999999999999999999998753
No 85
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=39.64 E-value=36 Score=28.24 Aligned_cols=47 Identities=9% Similarity=0.047 Sum_probs=39.4
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...++++.-.+...+ + -.++|+.+|++...|.+.....|++.++.
T Consensus 107 Lp~~~r~v~~l~~~~g~----s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 107 LPARQREAFLLRYWEDM----D----VAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred CCHHHHHHHHHHHHhcC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 89999999988666662 3 35799999999999999999999988764
No 86
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=39.26 E-value=30 Score=30.14 Aligned_cols=51 Identities=18% Similarity=0.272 Sum_probs=40.8
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCCC
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNSQ 292 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~~ 292 (303)
.||...++++.-.+.... + -.++|+.+|++...|.+.+...|++.++-...
T Consensus 141 ~Lp~~~r~v~~l~~~eg~--s------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~ 191 (194)
T PRK12531 141 RLPKAQRDVLQAVYLEEL--P------HQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDA 191 (194)
T ss_pred hCCHHHHHHHHHHHHcCC--C------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhh
Confidence 388899999987666553 2 34799999999999999999999998865443
No 87
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=39.19 E-value=34 Score=29.34 Aligned_cols=47 Identities=15% Similarity=0.114 Sum_probs=38.8
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.+...+ .-.++|+.+|++...|.++....|++.++.
T Consensus 136 L~~~~r~vl~l~~~~~~--------s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 136 LSPEERRVIEVLYYQGY--------THREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 88889999987666552 235799999999999999999999988753
No 88
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=39.10 E-value=24 Score=24.18 Aligned_cols=21 Identities=19% Similarity=0.232 Sum_probs=18.4
Q ss_pred HHHHHHHhCCChHHHhhhhHh
Q 022056 261 KAKLVEETGLQLKQINNWFIN 281 (303)
Q Consensus 261 k~~LA~~tgLs~kQI~nWF~N 281 (303)
...||+.+|+++..|..|..+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHhCCCcchhHHHhcC
Confidence 368999999999999999988
No 89
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=38.98 E-value=52 Score=27.04 Aligned_cols=47 Identities=6% Similarity=0.067 Sum_probs=31.6
Q ss_pred cCCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhh
Q 022056 231 RAGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRK 284 (303)
Q Consensus 231 kr~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~ 284 (303)
++++++.+.+.........+. .....+|+..|++..+|.+|..-.+.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g-------~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPG-------MTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCC-------CCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 345588887554444333331 23457899999999999999777664
No 90
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=38.89 E-value=30 Score=29.49 Aligned_cols=47 Identities=13% Similarity=0.128 Sum_probs=37.6
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.|... ++ -.++|+.+|++...|.+++...|++.++-
T Consensus 137 L~~~~r~v~~l~~~~g----~s----~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 137 LPPKYRMVIVLKYMED----LS----LKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHhHHhhhHHhcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 8888889987754444 22 35789999999999999999999988753
No 91
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=38.56 E-value=35 Score=29.48 Aligned_cols=47 Identities=11% Similarity=0.138 Sum_probs=38.8
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||+..+.+|.-.+.... .-..+|...|+++..|.+-+...|++.++.
T Consensus 132 L~~~~r~vl~l~~~~~~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 132 LSPAHREIIDLVYYHEK--------SVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 88889999977666552 235799999999999999999999988764
No 92
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=38.52 E-value=35 Score=29.09 Aligned_cols=47 Identities=17% Similarity=0.189 Sum_probs=39.3
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.+...+ + -.++|+.+|++...|.++..-.|++.++-
T Consensus 101 L~~~~r~v~~l~~~~g~----s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 101 LPDEYREAIRLTELEGL----S----QQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred CCHHHHHHHHHHHHcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 88888999988777663 2 35799999999999999999999988764
No 93
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=38.06 E-value=72 Score=31.37 Aligned_cols=46 Identities=11% Similarity=0.176 Sum_probs=36.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhHhhcHHHHHHhHHHHHHHHHHhhC
Q 022056 103 QELDNFLAQYLIVLCTFKEQLQQHVRVHAVEAVMGCREIENTLQALTG 150 (303)
Q Consensus 103 pELDqFMeaYc~vL~kykeEL~kp~~~~~~EA~~f~~~ie~qL~~l~~ 150 (303)
-+-|.||.-|| |.+|-.++.+-++--|++|-.-+..+-.|+.++|.
T Consensus 134 T~C~Hy~H~~C--laRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcp 179 (368)
T KOG4445|consen 134 TACDHYMHFAC--LARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCP 179 (368)
T ss_pred ehhHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhh
Confidence 47899999998 45566666666655568888889999999999985
No 94
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=37.89 E-value=33 Score=30.01 Aligned_cols=48 Identities=17% Similarity=0.072 Sum_probs=39.6
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
||...+.++.-.+...+ + -.++|+.+|++...|.++....|++.++-.
T Consensus 117 Lp~~~r~i~~L~~~~g~----s----~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 117 LPDDQREAIILVGASGF----A----YEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred CCHHHHHHHHHHHHcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 88888999877766663 2 237899999999999999999999988753
No 95
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=37.36 E-value=30 Score=23.45 Aligned_cols=23 Identities=13% Similarity=0.387 Sum_probs=17.0
Q ss_pred HHHHHHHhCCChHHHhhhhHhhh
Q 022056 261 KAKLVEETGLQLKQINNWFINQR 283 (303)
Q Consensus 261 k~~LA~~tgLs~kQI~nWF~N~R 283 (303)
...+|+.+|++...|.+|....+
T Consensus 20 ~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 20 IREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHHHCcCHHHHHHHHHHcc
Confidence 45899999999999999976544
No 96
>cd00131 PAX Paired Box domain
Probab=37.08 E-value=93 Score=26.04 Aligned_cols=45 Identities=13% Similarity=0.153 Sum_probs=30.7
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCC-------ChHHHhhhhHhh
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGL-------QLKQINNWFINQ 282 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgL-------s~kQI~nWF~N~ 282 (303)
+.......+..+..+| |.-|-.+-..+-...|+ +..+|+.||.|+
T Consensus 76 ~~~~~~~~i~~~v~~~---p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 76 ATPEVVKKIEIYKQEN---PGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CCHHHHHHHHHHHHHC---CCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 3444555566666766 78877776655335566 999999998764
No 97
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=37.07 E-value=75 Score=22.98 Aligned_cols=47 Identities=17% Similarity=0.266 Sum_probs=36.7
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhh
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQ 282 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~ 282 (303)
|+..++.+|..-+..= +.-+|-...-..||+..|++..-+..-+-+.
T Consensus 1 LT~~Q~e~L~~A~~~G-Yfd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 1 LTDRQREILKAAYELG-YFDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCHHHHHHHHHHHHcC-CCCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4667888898876654 4556889999999999999999988744443
No 98
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=37.00 E-value=37 Score=29.52 Aligned_cols=47 Identities=13% Similarity=0.109 Sum_probs=38.7
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.+...+ .-.++|+.+|++...|.++....|++.++-
T Consensus 137 L~~~~r~i~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 183 (195)
T PRK12532 137 LPENTARVFTLKEILGF--------SSDEIQQMCGISTSNYHTIMHRARESLRQC 183 (195)
T ss_pred CCHHHHHHhhhHHHhCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 88888899876655552 235899999999999999999999998874
No 99
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=36.83 E-value=48 Score=31.08 Aligned_cols=50 Identities=10% Similarity=-0.030 Sum_probs=40.8
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCCC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNSQ 292 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~~ 292 (303)
||..++.++.-.+...+ + -.++|+.+|++...|.+.+...|++.++..+.
T Consensus 116 L~~~~R~v~~L~~~~g~--s------~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~ 165 (293)
T PRK09636 116 LSPLERAAFLLHDVFGV--P------FDEIASTLGRSPAACRQLASRARKHVRAARPR 165 (293)
T ss_pred CCHHHHHHHHHHHHhCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCC
Confidence 88888888866555552 2 34789999999999999999999999987664
No 100
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=36.81 E-value=39 Score=29.30 Aligned_cols=48 Identities=15% Similarity=0.011 Sum_probs=40.0
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.||..++.++.-.+.... + -.++|+.+|+++..|.++....|++.++-
T Consensus 130 ~Lp~~~r~v~~L~~~~g~----s----~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 177 (185)
T PRK09649 130 DLTTDQREALLLTQLLGL----S----YADAAAVCGCPVGTIRSRVARARDALLAD 177 (185)
T ss_pred hCCHHHhHHhhhHHHcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 389999999977766663 2 34799999999999999999999999873
No 101
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=36.49 E-value=37 Score=29.24 Aligned_cols=48 Identities=17% Similarity=0.107 Sum_probs=38.9
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
||+..+.++.-.+...+ .-.++|+.+|++...|.+.....|++.++-.
T Consensus 123 L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 123 LNESNRQVFKYKVFYNL--------TYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 88889999977655552 1347999999999999999999999988753
No 102
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=36.34 E-value=80 Score=25.93 Aligned_cols=48 Identities=15% Similarity=0.216 Sum_probs=38.5
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
.|+...+++|.- +..+ |. ...+|+..+++.+.|.+|..|.|++..-.+
T Consensus 149 ~lt~~e~~vl~l-~~~g----~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~ 196 (211)
T PRK15369 149 LLTPRERQILKL-ITEG----YT----NRDIAEQLSISIKTVETHRLNMMRKLDVHK 196 (211)
T ss_pred CCCHHHHHHHHH-HHCC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence 488888888877 4555 32 468889999999999999999999987554
No 103
>PRK04217 hypothetical protein; Provisional
Probab=35.90 E-value=46 Score=27.60 Aligned_cols=49 Identities=8% Similarity=-0.054 Sum_probs=39.0
Q ss_pred CCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 233 GKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 233 ~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.+|+.+.++++..++.... .-.++|+.+|++...|.+.+...|++.+.-
T Consensus 41 ~~Lt~eereai~l~~~eGl--------S~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL--------TQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4477788888877766552 455799999999999999999999887653
No 104
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=35.76 E-value=41 Score=28.39 Aligned_cols=47 Identities=6% Similarity=0.033 Sum_probs=37.8
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...++++.--+.... .-..+|..+|++...|.++..-.|++.++.
T Consensus 120 L~~~~r~i~~l~~~~g~--------s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 120 LNDKYQTAIILRYYHDL--------TIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CCHHHhHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 88888888877666552 234789999999999999999999988753
No 105
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=35.55 E-value=42 Score=29.06 Aligned_cols=47 Identities=15% Similarity=0.058 Sum_probs=38.7
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||..++.++.-.+...+ + -.++|..+|++...|.+.....|++.++-
T Consensus 132 Lp~~~r~v~~l~~~~g~----s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 132 LPPRTGRVFMMREWLEL----E----TEEICQELQITATNAWVLLYRARMRLREC 178 (191)
T ss_pred CCHHHHHHHHHHHHcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 88889899877766552 2 35799999999999999999999988763
No 106
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=35.23 E-value=22 Score=24.16 Aligned_cols=21 Identities=5% Similarity=0.260 Sum_probs=18.9
Q ss_pred HHHHHhCCChHHHhhhhHhhh
Q 022056 263 KLVEETGLQLKQINNWFINQR 283 (303)
Q Consensus 263 ~LA~~tgLs~kQI~nWF~N~R 283 (303)
.||+.+|++...|+.|+.|.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998873
No 107
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=34.94 E-value=28 Score=23.62 Aligned_cols=23 Identities=22% Similarity=0.273 Sum_probs=19.5
Q ss_pred HHHHHHHhCCChHHHhhhhHhhh
Q 022056 261 KAKLVEETGLQLKQINNWFINQR 283 (303)
Q Consensus 261 k~~LA~~tgLs~kQI~nWF~N~R 283 (303)
-..||..+|+++..|+.|..+.+
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 35799999999999999986653
No 108
>PF15500 Toxin_39: Putative RNase-like toxin
Probab=34.66 E-value=94 Score=25.13 Aligned_cols=37 Identities=14% Similarity=0.108 Sum_probs=26.5
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHhhhHhhcHHHHHHhHHHHHH
Q 022056 100 HERQELDNFLAQYLIVLCTFKEQLQQHVRVHAVEAVMGCREIEN 143 (303)
Q Consensus 100 ~~dpELDqFMeaYc~vL~kykeEL~kp~~~~~~EA~~f~~~ie~ 143 (303)
+++|+|.+.|+. .+-+++..-++. ++||....+.+|.
T Consensus 45 ~a~p~lk~wne~-vq~~Rk~dp~~a------AdeaakLi~alE~ 81 (96)
T PF15500_consen 45 AADPALKAWNET-VQAKRKLDPKFA------ADEAAKLIQALET 81 (96)
T ss_pred ccCHHHHHHHHH-HHHHHhhchhhh------HHHHHHHHHHHHH
Confidence 689999999998 445556665665 4677766666664
No 109
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=34.65 E-value=36 Score=30.81 Aligned_cols=47 Identities=17% Similarity=0.213 Sum_probs=38.8
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.|.... .-..+|+.+|++...|.++....|++.++-
T Consensus 185 L~~~~r~vl~l~~~~g~--------s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 185 LPEREQLVLSLYYQEEL--------NLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CCHHHHHHHHhHhccCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 78888888877665442 346899999999999999999999998764
No 110
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=34.60 E-value=42 Score=28.38 Aligned_cols=48 Identities=10% Similarity=0.106 Sum_probs=39.9
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
||...+.+|.--+...+ + -.++|+.+|++...|.+..-..|++.++..
T Consensus 119 L~~~~r~vl~L~~~~g~----s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 119 LSPEHRAVLVRSYYRGW----S----TAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred CCHHHHHHHHHHHHcCC----C----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 89999999987766663 3 347999999999999999999999988753
No 111
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=34.54 E-value=44 Score=29.51 Aligned_cols=51 Identities=10% Similarity=0.033 Sum_probs=42.3
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCCCC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNSQS 293 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~~~ 293 (303)
||...+.++.--+..+. .-.++|+.+|+++..|.++....|++.++.....
T Consensus 134 Lp~~~r~v~~l~~~~g~--------s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 134 LPPERREALILTQVLGY--------TYEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred CCHHHHHHhhhHHHhCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 88889999877766663 2458999999999999999999999999875554
No 112
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=34.47 E-value=40 Score=29.27 Aligned_cols=47 Identities=17% Similarity=0.160 Sum_probs=38.7
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||..++.++.-.+... +| -.++|...|++...|.+.+...|++.++-
T Consensus 107 L~~~~r~i~~l~~~~g----~~----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (181)
T PRK09637 107 LPEKYAEALRLTELEG----LS----QKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153 (181)
T ss_pred CCHHHHHHHHHHHhcC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 8888999997766666 23 35789999999999999999999888763
No 113
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=34.29 E-value=51 Score=27.22 Aligned_cols=40 Identities=18% Similarity=0.332 Sum_probs=30.1
Q ss_pred hHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhh
Q 022056 239 TTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQ 282 (303)
Q Consensus 239 ~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~ 282 (303)
....+.+|...|...| -.-..||+.+|+++.++..+|...
T Consensus 10 ~i~~~~~~I~~~~~~~----~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 10 TIHSILDWIEDNLESP----LSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHhcCCC----CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4566778888885444 345678899999999999888754
No 114
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=33.99 E-value=46 Score=27.78 Aligned_cols=47 Identities=13% Similarity=0.170 Sum_probs=38.1
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||+..+.++.-.|.... + -.++|+.+|++...|.....-.|++.++-
T Consensus 110 L~~~~r~v~~l~~~~~~----s----~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 110 LPARTRYAFEMYRLHGE----T----QKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CCHHHHHHHHHHHHcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 88889999977666552 2 45799999999999999988888887754
No 115
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=33.96 E-value=78 Score=33.56 Aligned_cols=38 Identities=29% Similarity=0.447 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhhHhhcHHHHHHhHHHHHHHHHHhhC
Q 022056 106 DNFLAQYLIVLCTFKEQLQQHVRVHAVEAVMGCREIENTLQALTG 150 (303)
Q Consensus 106 DqFMeaYc~vL~kykeEL~kp~~~~~~EA~~f~~~ie~qL~~l~~ 150 (303)
.-|.|+|+.-=.+.++|+++| +-..|..++.||+.|..
T Consensus 569 ~vfrEqYi~~~dlV~~e~qrH-------~~~l~~~k~~QlQ~l~~ 606 (741)
T KOG4460|consen 569 QVFREQYILKQDLVKEEIQRH-------VKLLCDQKKKQLQDLSY 606 (741)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHH
Confidence 457778877777889999998 56899999999999963
No 116
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=33.94 E-value=45 Score=29.03 Aligned_cols=48 Identities=13% Similarity=0.084 Sum_probs=39.7
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.||...+.++.-.|..+. .-..+|+.+|++...|.+...-.|++.++-
T Consensus 131 ~L~~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 131 HLPEQTARVFMMREVLGF--------ESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred hCCHHHHHHHHHHHHhCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 388888899888766663 346899999999999999999999998764
No 117
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=33.84 E-value=47 Score=28.46 Aligned_cols=47 Identities=9% Similarity=0.126 Sum_probs=38.7
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.+..+. .-.++|+.+|++...|.+.....|++.++-
T Consensus 118 Lp~~~r~i~~l~~~e~~--------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 164 (179)
T PRK12543 118 LPYKLRQVIILRYLHDY--------SQEEIAQLLQIPIGTVKSRIHAALKKLRQK 164 (179)
T ss_pred CCHHHHHHHHHHHHccC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 88888888877666662 235799999999999999999999998763
No 118
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=33.72 E-value=46 Score=29.76 Aligned_cols=47 Identities=13% Similarity=0.240 Sum_probs=38.7
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
.||...++++.-.|... -.-.++|+.+|++...|..|....+++.++
T Consensus 178 ~L~~~~r~vl~l~y~~~--------~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFED--------KTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 38888999998876544 235689999999999999999999988764
No 119
>PRK10072 putative transcriptional regulator; Provisional
Probab=33.59 E-value=29 Score=28.01 Aligned_cols=23 Identities=9% Similarity=0.284 Sum_probs=20.4
Q ss_pred HHHHHHHhCCChHHHhhhhHhhh
Q 022056 261 KAKLVEETGLQLKQINNWFINQR 283 (303)
Q Consensus 261 k~~LA~~tgLs~kQI~nWF~N~R 283 (303)
...||+.+|++...|++|...+|
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56899999999999999998765
No 120
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=33.24 E-value=34 Score=24.61 Aligned_cols=18 Identities=6% Similarity=0.152 Sum_probs=16.2
Q ss_pred HHHHHHhCCChHHHhhhh
Q 022056 262 AKLVEETGLQLKQINNWF 279 (303)
Q Consensus 262 ~~LA~~tgLs~kQI~nWF 279 (303)
.++|+.+|++..+|+.|-
T Consensus 4 ~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp HHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 478999999999999994
No 121
>PF12022 DUF3510: Domain of unknown function (DUF3510); InterPro: IPR024603 The COG complex comprises eight proteins (COG1-8) and plays critical roles in Golgi structure and function []. This uncharacterised domain is found in the C-terminal of COG complex subunit 2 proteins.
Probab=33.23 E-value=2.4e+02 Score=23.46 Aligned_cols=19 Identities=26% Similarity=0.413 Sum_probs=14.9
Q ss_pred HHHHHhHHHHHHHHHHhhC
Q 022056 132 VEAVMGCREIENTLQALTG 150 (303)
Q Consensus 132 ~EA~~f~~~ie~qL~~l~~ 150 (303)
.|...-.++.|..|+-|-.
T Consensus 80 ~evL~sv~KtEeSL~rlkk 98 (125)
T PF12022_consen 80 SEVLTSVRKTEESLKRLKK 98 (125)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4666778889999998854
No 122
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=32.71 E-value=38 Score=30.98 Aligned_cols=47 Identities=9% Similarity=0.157 Sum_probs=38.4
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||..++.++.-.|...+ .-.++|+.+|++...|.+++...|++.++.
T Consensus 172 Lp~~~R~v~~L~~~eg~--------s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~ 218 (233)
T PRK12538 172 LPEQQRIAVILSYHENM--------SNGEIAEVMDTTVAAVESLLKRGRQQLRDL 218 (233)
T ss_pred CCHHHHHHhhhHHhcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 78888888776665552 235799999999999999999999998875
No 123
>PF05190 MutS_IV: MutS family domain IV C-terminus.; InterPro: IPR007861 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the clamp domain (domain 4) found in proteins of the MutS family. The clamp domain is inserted within the core domain at the top of the lever helices. It has a beta-sheet structure [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B 1WBD_A 1WB9_A 3K0S_A 1OH6_A ....
Probab=32.70 E-value=77 Score=23.81 Aligned_cols=25 Identities=24% Similarity=0.284 Sum_probs=20.1
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHh
Q 022056 100 HERQELDNFLAQYLIVLCTFKEQLQ 124 (303)
Q Consensus 100 ~~dpELDqFMeaYc~vL~kykeEL~ 124 (303)
|-|++||.....|..+.....+.+.
T Consensus 1 g~d~~Ld~~~~~~~~~~~~l~~~~~ 25 (92)
T PF05190_consen 1 GFDEELDELREEYEEIEEELEELLE 25 (92)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4589999999999888777766664
No 124
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=32.49 E-value=53 Score=27.41 Aligned_cols=45 Identities=13% Similarity=0.164 Sum_probs=37.0
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNW 287 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~k 287 (303)
||+.++.++.-.+.... + -.++|+.+|++...|.++....+++..
T Consensus 114 L~~~~r~v~~L~~~~g~----s----~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 114 LPPLVKRAFLLAQVDGL----G----YGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred CCHHHHHHHHHHHHcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 89999999977766663 2 347999999999999999999888754
No 125
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=32.31 E-value=63 Score=30.24 Aligned_cols=50 Identities=10% Similarity=-0.019 Sum_probs=39.9
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCCC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNSQ 292 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~~ 292 (303)
||..++.++.-.+...+ + -.++|+.+|+++..|.+.+...|++.+...+.
T Consensus 109 L~~~~R~v~~L~~~~g~----s----~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~~ 158 (281)
T TIGR02957 109 LSPLERAVFVLREVFDY----P----YEEIASIVGKSEANCRQLVSRARRHLDARRPR 158 (281)
T ss_pred CCHHHHHHHHHHHHcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCC
Confidence 78888888866544442 2 34789999999999999999999999887654
No 126
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=32.29 E-value=1.4e+02 Score=26.85 Aligned_cols=47 Identities=15% Similarity=0.204 Sum_probs=39.0
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHhhhHhhcHHHH-HHhHHHHHHHHHHhhC
Q 022056 101 ERQELDNFLAQYLIVLCTFKEQLQQHVRVHAVEA-VMGCREIENTLQALTG 150 (303)
Q Consensus 101 ~dpELDqFMeaYc~vL~kykeEL~kp~~~~~~EA-~~f~~~ie~qL~~l~~ 150 (303)
+=-|||-.+.++-.++..|++.++-.+. .+| ..|+..|..||-.+..
T Consensus 102 DItELDVvL~~FEk~~~eYkq~ieS~~c---r~AI~~F~~~~keqL~~~i~ 149 (175)
T PF13097_consen 102 DITELDVVLSAFEKTALEYKQSIESKIC---RKAINKFYSNFKEQLIEMIK 149 (175)
T ss_pred cchHHHHHHHHHHHHHHHHHHhhccHHH---HHHHHHHHHHHHHHHHHHHH
Confidence 5579999999999999999999998762 344 5689999999988763
No 127
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=32.29 E-value=54 Score=30.04 Aligned_cols=47 Identities=11% Similarity=0.138 Sum_probs=39.0
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.+|.-.|.... + -.++|+.+|++...|.+|....+++.++.
T Consensus 206 L~~~~r~vl~l~~~~g~--s------~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 206 LSDREKSIIQCTFIENL--S------QKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred CCHHHHHHHHHHHhCCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 88889999988766552 2 36899999999999999999999988754
No 128
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=32.23 E-value=22 Score=30.85 Aligned_cols=47 Identities=13% Similarity=0.113 Sum_probs=37.1
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.|.... + -..+|+.+|++...|.++....|++.++-
T Consensus 140 L~~~~r~i~~l~~~~g~----s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 140 LPDEQREVFLLREHGDL----E----LEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred CCHhHhhheeeehccCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 77777788876554442 2 34789999999999999999999998864
No 129
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=32.17 E-value=40 Score=21.52 Aligned_cols=21 Identities=19% Similarity=0.222 Sum_probs=18.7
Q ss_pred HHHHHHhCCChHHHhhhhHhh
Q 022056 262 AKLVEETGLQLKQINNWFINQ 282 (303)
Q Consensus 262 ~~LA~~tgLs~kQI~nWF~N~ 282 (303)
..+|+.+|+++..|++|..+.
T Consensus 16 ~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 16 EELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHCCCHHHHHHHHcCC
Confidence 488999999999999998875
No 130
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=32.14 E-value=1e+02 Score=20.93 Aligned_cols=40 Identities=13% Similarity=0.278 Sum_probs=26.0
Q ss_pred CCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhh
Q 022056 232 AGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWF 279 (303)
Q Consensus 232 r~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF 279 (303)
+.+++++..+.+..-+..- .....+|+.+|++...|-.++
T Consensus 3 p~~~~~~~~~~i~~l~~~G--------~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 3 PPKLSKEQIEEIKELYAEG--------MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSSHCCHHHHHHHHHTT----------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHCC--------CCHHHHHHHHCcCHHHHHHHH
Confidence 3457776555555544433 346789999999999998775
No 131
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=31.68 E-value=46 Score=30.12 Aligned_cols=48 Identities=15% Similarity=0.102 Sum_probs=40.7
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.||...+.++.-.|..++ + -.++|+.+|++...|.++....|++.++.
T Consensus 134 ~Lp~~~R~v~~L~y~eg~----s----~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 134 KLPVEYREVLVLRELEDM----S----YREIAAIADVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred cCCHHHHhHhhhHHhcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 388889999988877773 3 24789999999999999999999998885
No 132
>PF07425 Pardaxin: Pardaxin; InterPro: IPR009990 This family consists of several Pardaxin proteins. Pardaxin, a 33-amino-acid pore-forming polypeptide toxin isolated from the Red Sea Moses sole Pardachirus marmoratus, has a helix-hinge-helix structure. This is a common structural motif found both in antibacterial peptides that can act selectively on bacterial membranes (e.g., cecropin), and in cytotoxic peptides that can lyse both mammalian and bacterial cells (e.g., melittin). Pardaxin possesses a high antibacterial activity with a significantly reduced haemolytic activity towards human red blood cells compared with melittin []. Pardaxin has also been found to have a shark repellent action [].; GO: 0005576 extracellular region; PDB: 1XC0_A 2KNS_A.
Probab=31.47 E-value=30 Score=22.31 Aligned_cols=22 Identities=41% Similarity=0.579 Sum_probs=17.4
Q ss_pred HHHHHHhCCChHHHHHHHHhhh
Q 022056 36 IKAEIASHPLYEQLLAAHVSCL 57 (303)
Q Consensus 36 iKa~I~sHPlYp~Ll~A~i~C~ 57 (303)
+-.+|++.|||.-||.|--..+
T Consensus 5 lipkiissplfktllsavgsal 26 (33)
T PF07425_consen 5 LIPKIISSPLFKTLLSAVGSAL 26 (33)
T ss_dssp CHHHHCCTTTCHHHHHHHHHHC
T ss_pred hhhHHHccHHHHHHHHHHHHHH
Confidence 3468999999999998865544
No 133
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=31.40 E-value=49 Score=28.11 Aligned_cols=47 Identities=13% Similarity=0.120 Sum_probs=36.2
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.+|.-.+... ..-.++|..+|++...|.++....|++.++.
T Consensus 137 L~~~~r~il~l~~~~~--------~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 137 LPEKYRTVIVLKYIED--------LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHhhhHHhhC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 7777888885544333 2245799999999999999999999988753
No 134
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=31.34 E-value=78 Score=22.26 Aligned_cols=47 Identities=21% Similarity=0.157 Sum_probs=33.8
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
|++...++|.-+..-. ...++|...|++++.|.++..|.++|..-.+
T Consensus 4 LT~~E~~vl~~l~~G~---------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~ 50 (58)
T PF00196_consen 4 LTERELEVLRLLAQGM---------SNKEIAEELGISEKTVKSHRRRIMKKLGVKN 50 (58)
T ss_dssp S-HHHHHHHHHHHTTS----------HHHHHHHHTSHHHHHHHHHHHHHHHHT-SS
T ss_pred cCHHHHHHHHHHHhcC---------CcchhHHhcCcchhhHHHHHHHHHHHhCCCC
Confidence 6666677775543322 3457899999999999999999999987554
No 135
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=31.31 E-value=70 Score=21.17 Aligned_cols=47 Identities=15% Similarity=0.187 Sum_probs=34.2
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.|+....+++.. +... + ....+|+.+|++...|..|....+.+..-.
T Consensus 3 ~l~~~e~~i~~~-~~~g----~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 3 SLTPREREVLRL-LAEG----L----TNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHHHH-HHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 467777777644 3322 2 346889999999999999999888877644
No 136
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=31.30 E-value=48 Score=30.69 Aligned_cols=47 Identities=11% Similarity=0.210 Sum_probs=39.3
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.+..+. .-.++|..+|++...|.+++...|++.++.
T Consensus 162 Lp~~~R~v~~L~~~eg~--------S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~ 208 (244)
T TIGR03001 162 LSERERHLLRLHFVDGL--------SMDRIGAMYQVHRSTVSRWVAQARERLLER 208 (244)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 88888899887777663 235799999999999999999999988764
No 137
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=31.28 E-value=45 Score=28.62 Aligned_cols=47 Identities=13% Similarity=0.181 Sum_probs=38.4
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
+||+.++.++.-.+.... + -.++|+.+|++...|.++..-.|++.++
T Consensus 127 ~L~~~~r~v~~l~~~~g~----s----~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 127 SLPIKYREVIYLFYYEEL----S----IKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred hCCHHHhhHhHhHHhcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 388889999877666552 2 3479999999999999999999998875
No 138
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=30.97 E-value=56 Score=28.14 Aligned_cols=47 Identities=11% Similarity=-0.002 Sum_probs=39.3
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...++++.-.+.... .-..+|+.+|++...|.++.-..|++.++-
T Consensus 132 L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 132 LPEKMRLAIQAVKLEGL--------SVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred CCHHHHHHHHHHHHcCC--------cHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 89999999987666553 235799999999999999999999998864
No 139
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=30.97 E-value=26 Score=30.46 Aligned_cols=47 Identities=13% Similarity=0.063 Sum_probs=37.6
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.+.... .-.++|+.+|++...|.++..-.|++.++-
T Consensus 132 Lp~~~r~i~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 178 (193)
T TIGR02947 132 LPEEFRQAVYLADVEGF--------AYKEIAEIMGTPIGTVMSRLHRGRKQLRKQ 178 (193)
T ss_pred CCHHHhhheeehhhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 78888888766555552 235799999999999999999999998864
No 140
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=30.59 E-value=53 Score=29.23 Aligned_cols=47 Identities=11% Similarity=0.121 Sum_probs=37.7
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.+...+ + -.++|+.+|++...|.++..-.|++.++-
T Consensus 139 L~~~~r~v~~L~~~~g~----s----~~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 139 LPPEFRAAVVLCDIEGL----S----YEEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred CCHHHHHHHHHHHHcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 78888887766655552 2 34799999999999999999999998864
No 141
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=30.50 E-value=56 Score=29.15 Aligned_cols=48 Identities=15% Similarity=0.131 Sum_probs=39.7
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.||...+.++.-.|.... + -.++|+.+|++...|.++..-.|++.++.
T Consensus 148 ~L~~~~r~v~~L~~~~g~----s----~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 148 GLPAKYARVFMMREFIEL----E----TNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred hCCHHHHHHHHHHHHcCC----C----HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 388888888877776663 2 35799999999999999999999998864
No 142
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=30.44 E-value=55 Score=27.78 Aligned_cols=47 Identities=11% Similarity=0.146 Sum_probs=37.4
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...++++.-.|.... .-.++|+.+|++...|.++....|++.++.
T Consensus 120 L~~~~r~i~~l~~~~~~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 120 LNEKYKTVLVLYYYEQY--------SYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 78878888866655552 235799999999999999999999988764
No 143
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=30.21 E-value=68 Score=27.54 Aligned_cols=47 Identities=4% Similarity=-0.007 Sum_probs=38.7
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||+.++.++.-.+...+ + -.++|+.+|+++..|.+.+..++.+....
T Consensus 128 Lp~~~R~v~~L~~~~g~----s----~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 128 LRPRVKQAFLMATLDGM----K----QKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred CCHHHHHHHHHHHHcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 89999999988766663 2 35799999999999999999988887654
No 144
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=29.84 E-value=52 Score=29.60 Aligned_cols=51 Identities=12% Similarity=0.095 Sum_probs=37.9
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.|..+ +-..-.-.++|+.+|++...|.++...+|++.++.
T Consensus 179 Lp~~~R~v~~L~y~l~----~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 179 LSDREKQIMELRFGLN----GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred CCHHHHHHHHHHhccC----CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 8888888887655211 01112345899999999999999999999998864
No 145
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=29.66 E-value=51 Score=21.87 Aligned_cols=20 Identities=15% Similarity=0.165 Sum_probs=17.2
Q ss_pred HHHHHHhCCChHHHhhhhHh
Q 022056 262 AKLVEETGLQLKQINNWFIN 281 (303)
Q Consensus 262 ~~LA~~tgLs~kQI~nWF~N 281 (303)
.++|+.+|+++..|..|..+
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 47899999999999999543
No 146
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=29.45 E-value=57 Score=31.05 Aligned_cols=49 Identities=16% Similarity=0.046 Sum_probs=40.5
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNS 291 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~ 291 (303)
||...+.++.-.+...+ + -.++|+.+|++...|.+.....|++.++..|
T Consensus 154 Lp~~~R~v~~L~~~~g~----s----~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~ 202 (339)
T PRK08241 154 LPPRQRAVLILRDVLGW----S----AAEVAELLDTSVAAVNSALQRARATLAERGP 202 (339)
T ss_pred CCHHHhhhhhhHHhhCC----C----HHHHHHHhCCCHHHHHHHHHHHHHHHhhcCC
Confidence 88888888877666663 2 3479999999999999999999999999654
No 147
>PF12362 DUF3646: DNA polymerase III gamma and tau subunits C terminal; InterPro: IPR022107 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF00004 from PFAM. The proteins in this family are frequently annotated as the gamma and tau subunits of DNA polymerase III, however there is little accompanying literature to back this up.
Probab=29.44 E-value=25 Score=29.45 Aligned_cols=22 Identities=32% Similarity=0.452 Sum_probs=19.3
Q ss_pred hHHHHHHHHHhCCChHHHHHHH
Q 022056 32 TVQLIKAEIASHPLYEQLLAAH 53 (303)
Q Consensus 32 ~~~~iKa~I~sHPlYp~Ll~A~ 53 (303)
..+..++.+..||++...|++|
T Consensus 87 ~~~~~~~~a~~~P~V~avL~~F 108 (117)
T PF12362_consen 87 AKEARRAAARAHPLVKAVLAAF 108 (117)
T ss_pred HHHHHHHHHHhCcHHHHHHHHC
Confidence 3567899999999999999886
No 148
>PF13551 HTH_29: Winged helix-turn helix
Probab=29.17 E-value=2e+02 Score=22.04 Aligned_cols=46 Identities=17% Similarity=0.110 Sum_probs=29.3
Q ss_pred CCcchHHHHHHHHHHcCCCC--CCCHHHHHH-H-HHHh--CCChHHHhhhhH
Q 022056 235 LPGDTTSVLKNWWQQHSKWP--YPTEDDKAK-L-VEET--GLQLKQINNWFI 280 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~P--YPs~~ek~~-L-A~~t--gLs~kQI~nWF~ 280 (303)
++.+..+.|.+++..+.... ..+...-.. | .+.+ .++...|..|+.
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 89999999999999883111 123333332 3 2222 478888888874
No 149
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=28.99 E-value=53 Score=30.05 Aligned_cols=48 Identities=8% Similarity=0.099 Sum_probs=39.5
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.||...+.++.-.|.... .-.++|+.+|++...|..+....+++.++.
T Consensus 205 ~L~~~~r~ii~l~~~~g~--------s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 205 ILSEREKSIIHCTFEENL--------SQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred cCCHHHHHHHHHHHcCCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 388889999988776553 236899999999999999999999988753
No 150
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=28.97 E-value=58 Score=29.14 Aligned_cols=46 Identities=15% Similarity=0.162 Sum_probs=38.7
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
||...+++|...|.... .-..+|+.+|++...|..+....+++.++
T Consensus 176 L~~~~r~il~l~y~~~~--------s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 176 LSEREQLVLSLYYYEEL--------NLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CCHHHHHHHHHHHhCCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 88889999988776552 24689999999999999999999988775
No 151
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=28.72 E-value=59 Score=29.79 Aligned_cols=46 Identities=9% Similarity=0.081 Sum_probs=38.2
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
||...+.++.-.|.... .-..+|..+|++...|.+++...|++.++
T Consensus 202 L~~~~r~vl~l~~~~~~--------s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 202 LSEKEQLVISLFYKEEL--------TLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CCHHHHHHHHHHHhcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 88888899987665542 24689999999999999999999998875
No 152
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=28.63 E-value=57 Score=28.37 Aligned_cols=49 Identities=14% Similarity=-0.007 Sum_probs=40.2
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNS 291 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~ 291 (303)
||...+.++.-.+.... .-.++|+.+|++...|.+...-.|++.++...
T Consensus 112 Lp~~~R~v~~L~~~~g~--------s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 112 LPQDQREALILVGASGF--------SYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CCHHHHHHhhHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 78889999877766553 23479999999999999999999999987644
No 153
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=28.60 E-value=59 Score=28.33 Aligned_cols=49 Identities=10% Similarity=0.040 Sum_probs=40.4
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
.||..++.++.-.+.... + -.++|+.+|++...|.++..-.|++.++-.
T Consensus 111 ~Lp~~~R~v~~L~~~eg~----s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAIEGL----S----YQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHHcCC----C----HHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 389999999988777662 3 347999999999999999999999887653
No 154
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=28.50 E-value=56 Score=25.01 Aligned_cols=6 Identities=50% Similarity=1.104 Sum_probs=2.3
Q ss_pred HHHHHH
Q 022056 104 ELDNFL 109 (303)
Q Consensus 104 ELDqFM 109 (303)
|||+||
T Consensus 48 ELD~Ym 53 (74)
T PF13865_consen 48 ELDAYM 53 (74)
T ss_pred HHHHHH
Confidence 333333
No 155
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=28.04 E-value=61 Score=27.77 Aligned_cols=46 Identities=9% Similarity=0.166 Sum_probs=37.6
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
||+..+.++...|..+. + -.++|..+|++...|.+.....|++.++
T Consensus 138 L~~~~r~i~~l~~~~g~----s----~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 138 LEPPRSELIRTAFFEGI----T----YEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CCHHHHHHHHHHHHcCC----C----HHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 78888888877766552 2 3478999999999999999999998775
No 156
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=27.94 E-value=20 Score=32.99 Aligned_cols=28 Identities=39% Similarity=0.705 Sum_probs=24.4
Q ss_pred HHHHHHHHHhCCChHHHHHHHHhhhcccCCCc
Q 022056 33 VQLIKAEIASHPLYEQLLAAHVSCLRVATPID 64 (303)
Q Consensus 33 ~~~iKa~I~sHPlYp~Ll~A~i~C~KVgaP~e 64 (303)
...||..|..||++.+||+||+ ||.|.-
T Consensus 110 ~~LL~e~~~~~pl~~rLVAAYl----iG~~v~ 137 (207)
T PF11288_consen 110 LRLLKEEIAGDPLRKRLVAAYL----IGYPVT 137 (207)
T ss_pred HHHHHHHhcCchHHhhhheeee----cCcccc
Confidence 4679999999999999999998 777753
No 157
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=27.93 E-value=67 Score=26.74 Aligned_cols=47 Identities=13% Similarity=0.137 Sum_probs=39.2
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.+..+. .-.++|..+|++...|.+....+|++.++.
T Consensus 106 L~~~~r~v~~l~~~~~~--------s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 106 LPPACRDSFLLRKLEGL--------SHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 88899999988776663 235799999999999999999999888764
No 158
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=27.87 E-value=59 Score=31.45 Aligned_cols=53 Identities=13% Similarity=0.107 Sum_probs=42.0
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
.||...+.+|...|..+ |-..-.-..+|..+|++...|..+...++++.|+-.
T Consensus 262 ~L~~~~R~vl~lrygL~----~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLL----GYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccC----CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 38888999998766433 223345578999999999999999999999998753
No 159
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=27.77 E-value=73 Score=30.23 Aligned_cols=50 Identities=14% Similarity=0.011 Sum_probs=39.7
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCCC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNSQ 292 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~~ 292 (303)
||+.++.++.-.+...+ + -.++|+.+|+++..|...+.-.|++.+...|.
T Consensus 119 L~p~~R~vf~L~~~~g~--s------~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~~ 168 (290)
T PRK09635 119 LGPAERVVFVLHEIFGL--P------YQQIATTIGSQASTCRQLAHRARRKINESRIA 168 (290)
T ss_pred CCHHHHHHhhHHHHhCC--C------HHHHHHHHCcCHHHHHHHHHHHHHHHHhhCCC
Confidence 78888887765555442 2 24789999999999999999999999987664
No 160
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=27.76 E-value=1.2e+02 Score=21.29 Aligned_cols=41 Identities=15% Similarity=0.117 Sum_probs=28.6
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhh
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQ 282 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~ 282 (303)
|+.+.+-.|-=.+.++ |++.+ .||...|++.+.|++||..-
T Consensus 3 Ls~~d~lll~L~~LR~----~~~~~---~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 3 LSLEDQLLLTLMYLRL----NLTFQ---DLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred CCHHHHHHHHHHHHHc----CCcHh---HHhhheeecHHHHHHHHHHH
Confidence 5555555555555555 56644 68888999999999998753
No 161
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=27.65 E-value=50 Score=20.82 Aligned_cols=22 Identities=14% Similarity=0.217 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChHHHhhhhHhh
Q 022056 261 KAKLVEETGLQLKQINNWFINQ 282 (303)
Q Consensus 261 k~~LA~~tgLs~kQI~nWF~N~ 282 (303)
...+|+.+|++..+|..|..+.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4488999999999999997654
No 162
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=27.34 E-value=61 Score=30.03 Aligned_cols=47 Identities=13% Similarity=0.142 Sum_probs=38.9
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.|.... .-..+|..+|++...|.......+++.++.
T Consensus 213 L~~~~r~vl~l~~~~~~--------s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 213 LPEREKKVLILYYYEDL--------TLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 88888899988776552 246899999999999999999999888753
No 163
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=27.32 E-value=61 Score=27.92 Aligned_cols=47 Identities=11% Similarity=0.066 Sum_probs=36.8
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.+... |+ -.++|+.+|+++..|.+.....|++.++-
T Consensus 139 L~~~~r~v~~l~~~~g----~s----~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 185 (193)
T PRK11923 139 LPEDLRTALTLREFDG----LS----YEDIASVMQCPVGTVRSRIFRAREAIDKA 185 (193)
T ss_pred CCHHHhHHHhhHHhcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 7777877776644444 33 35799999999999999999999998763
No 164
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=27.17 E-value=66 Score=28.30 Aligned_cols=47 Identities=15% Similarity=0.062 Sum_probs=39.2
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.+...+ + -.++|+.+|++...|.+....+|++.++-
T Consensus 140 Lp~~~r~v~~L~~~eg~----s----~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 186 (201)
T PRK12545 140 LPEQIGRVFMMREFLDF----E----IDDICTELTLTANHCSVLLYRARTRLRTC 186 (201)
T ss_pred CCHHHHHHHHHHHHcCC----C----HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 88889999887766663 2 34789999999999999999999998874
No 165
>PHA01976 helix-turn-helix protein
Probab=26.78 E-value=48 Score=23.71 Aligned_cols=22 Identities=14% Similarity=0.296 Sum_probs=18.8
Q ss_pred HHHHHHHhCCChHHHhhhhHhh
Q 022056 261 KAKLVEETGLQLKQINNWFINQ 282 (303)
Q Consensus 261 k~~LA~~tgLs~kQI~nWF~N~ 282 (303)
..+||+.+|++...|.+|....
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 3579999999999999998654
No 166
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=26.73 E-value=72 Score=28.61 Aligned_cols=47 Identities=11% Similarity=0.117 Sum_probs=38.3
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
.||...+.++...|... ..-.++|+.+|+++..|..+-....+|.++
T Consensus 183 ~L~~~e~~i~~~~~~~~--------~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 183 KLDERERQIIMLRYFKD--------KTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred cCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 48888999987766543 346789999999999999999888888764
No 167
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=26.33 E-value=57 Score=21.72 Aligned_cols=19 Identities=5% Similarity=0.163 Sum_probs=15.2
Q ss_pred HHHHHHhCCChHHHhhhhH
Q 022056 262 AKLVEETGLQLKQINNWFI 280 (303)
Q Consensus 262 ~~LA~~tgLs~kQI~nWF~ 280 (303)
-++|+.+|++.+.|..|=.
T Consensus 3 ~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHH
Confidence 3689999999999999943
No 168
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=26.18 E-value=69 Score=27.24 Aligned_cols=30 Identities=33% Similarity=0.719 Sum_probs=24.5
Q ss_pred HHHHHHHhCCChHHHhhhhHhhhhhccccCCCC
Q 022056 261 KAKLVEETGLQLKQINNWFINQRKRNWHSNSQS 293 (303)
Q Consensus 261 k~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~~~ 293 (303)
.++||..||++...||-|. |+-.|+..|..
T Consensus 3 ~eELA~~tG~srQTINrWv---RkegW~T~p~p 32 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWV---RKEGWKTEPKP 32 (122)
T ss_pred HHHHHHHhCccHHHHHHHH---HhcCceeccCC
Confidence 4689999999999999995 67777766654
No 169
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=25.98 E-value=79 Score=26.32 Aligned_cols=47 Identities=15% Similarity=0.092 Sum_probs=37.8
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
.||...+.++.-.|... ++ -..+|+.+|++...|.+...-.|++.++
T Consensus 122 ~L~~~~r~vl~l~~~~g----~s----~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQN----LP----IAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHhcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 38888999998866655 22 3579999999999999999888888775
No 170
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=25.92 E-value=56 Score=27.84 Aligned_cols=45 Identities=9% Similarity=0.161 Sum_probs=35.6
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNW 287 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~k 287 (303)
||+..+.++.-.+..+. .-.++|+.+|++...|.++...++.+.+
T Consensus 120 L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 120 LNGKTREAFLLSQLDGL--------TYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred CCHHHhHHhhhhhccCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 78888888776655552 2458999999999999999988887654
No 171
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=25.90 E-value=49 Score=24.33 Aligned_cols=23 Identities=13% Similarity=0.198 Sum_probs=19.7
Q ss_pred HHHHHHHhCCChHHHhhhhHhhh
Q 022056 261 KAKLVEETGLQLKQINNWFINQR 283 (303)
Q Consensus 261 k~~LA~~tgLs~kQI~nWF~N~R 283 (303)
...||+.+|++...|+.|+.+.+
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 35799999999999999997654
No 172
>PRK06930 positive control sigma-like factor; Validated
Probab=25.82 E-value=75 Score=27.99 Aligned_cols=48 Identities=6% Similarity=0.001 Sum_probs=38.4
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.||...+.++.-.|.... .-..+|+.+|++...|.+++...|++.++.
T Consensus 114 ~L~~rer~V~~L~~~eg~--------s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGL--------SYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 388888898887665552 235789999999999999999999987753
No 173
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=25.53 E-value=50 Score=28.86 Aligned_cols=29 Identities=10% Similarity=0.183 Sum_probs=24.7
Q ss_pred hhccCCCCCcchHHHHHHHHHHcCCCCCC
Q 022056 228 RKRRAGKLPGDTTSVLKNWWQQHSKWPYP 256 (303)
Q Consensus 228 kkrkr~~lpk~~~~~L~~wf~~h~~~PYP 256 (303)
...+-+.|+.++...|..+...++..++|
T Consensus 49 ~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP 77 (149)
T PRK04053 49 PNAKLGYLSDEEIEKIEEALEDPAEEGIP 77 (149)
T ss_pred CCCccCcCCHHHHHHHHHHHHhhccccCc
Confidence 45566889999999999999988777888
No 174
>PF05821 NDUF_B8: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8); InterPro: IPR008699 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of several eukaryotic NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI) proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits [].; GO: 0003954 NADH dehydrogenase activity, 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=25.40 E-value=65 Score=29.02 Aligned_cols=22 Identities=32% Similarity=0.693 Sum_probs=19.3
Q ss_pred CCC-CHHHHHHHHHHhCCChHHH
Q 022056 254 PYP-TEDDKAKLVEETGLQLKQI 275 (303)
Q Consensus 254 PYP-s~~ek~~LA~~tgLs~kQI 275 (303)
||| |++||...|++.||.++.-
T Consensus 35 pyP~t~eer~aaAkKY~l~pedY 57 (179)
T PF05821_consen 35 PYPKTPEERAAAAKKYGLRPEDY 57 (179)
T ss_pred CCCCCHHHHHHHHHHcCCCHHHc
Confidence 898 7899999999999987753
No 175
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=25.34 E-value=78 Score=29.74 Aligned_cols=49 Identities=18% Similarity=0.026 Sum_probs=40.0
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccCC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSNS 291 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~~ 291 (303)
||..++.++.-.+...+ + -.++|+.+|++...|.+.+.-.|++.++...
T Consensus 143 Lp~~~R~v~~L~~~~g~----s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 143 LPPRQRAVLLLRDVLGW----R----AAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred CCHHHhhHhhhHHHhCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 88889898877666552 2 3479999999999999999999999988644
No 176
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=25.26 E-value=54 Score=29.32 Aligned_cols=40 Identities=23% Similarity=0.575 Sum_probs=30.8
Q ss_pred CCcchHHHHHHHHHHcCCCCCCC-HHHHHHHHHHhCCChHH
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPT-EDDKAKLVEETGLQLKQ 274 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs-~~ek~~LA~~tgLs~kQ 274 (303)
......+..-.|...|+-.|||+ ++||..-|++.||-+..
T Consensus 21 v~~~g~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEd 61 (186)
T KOG4040|consen 21 VMPRGPRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPED 61 (186)
T ss_pred ccccccccccccccccCCCCCCCCHHHHHHHHHHhCCCHhh
Confidence 33445566678988898889995 77888999999987664
No 177
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=25.25 E-value=90 Score=26.39 Aligned_cols=46 Identities=15% Similarity=0.230 Sum_probs=37.3
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNW 287 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~k 287 (303)
.||...+.++.-.+.+.+ + -.++|+.+|++...|.++..++++..+
T Consensus 118 ~L~~~~r~v~~L~~~eg~----s----~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 118 GLSGKARAAFLMSQLEGL----T----YVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred hCCHHHHHHHHHHHHcCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 388889999987777663 2 347899999999999999988887755
No 178
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=24.94 E-value=72 Score=29.88 Aligned_cols=52 Identities=13% Similarity=0.112 Sum_probs=40.8
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.||...+.+|.-.|..+ |-..-.-.++|..+|++...|..+.-.+|++.++-
T Consensus 222 ~Lp~~~R~Vl~l~ygL~----~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~ 273 (285)
T TIGR02394 222 ELNERQREVLARRFGLL----GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRI 273 (285)
T ss_pred cCCHHHHHHHHHHhCCC----CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 38999999998776222 12223467899999999999999999999998864
No 179
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=24.44 E-value=78 Score=27.49 Aligned_cols=45 Identities=18% Similarity=0.185 Sum_probs=35.8
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
||...+.++.- +... |+ -.++|..+|+++..|.+.+...|++.++
T Consensus 156 L~~~~r~vl~l-~~e~----~s----~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 156 LSELEKEVLEL-YLDG----KS----YQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred CCHHHHHHHHH-HHcc----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 77778888877 4444 22 3478999999999999999999998876
No 180
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=24.10 E-value=78 Score=20.37 Aligned_cols=22 Identities=14% Similarity=0.362 Sum_probs=19.0
Q ss_pred HHHHHHhCCChHHHhhhhHhhh
Q 022056 262 AKLVEETGLQLKQINNWFINQR 283 (303)
Q Consensus 262 ~~LA~~tgLs~kQI~nWF~N~R 283 (303)
.++|+.+|++...|..|..+-+
T Consensus 4 ~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 4 KEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHcCC
Confidence 5789999999999999987654
No 181
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=23.99 E-value=78 Score=26.32 Aligned_cols=27 Identities=15% Similarity=0.292 Sum_probs=23.9
Q ss_pred CCCHHHHHHHHHHhCCChHHHhhhhHh
Q 022056 255 YPTEDDKAKLVEETGLQLKQINNWFIN 281 (303)
Q Consensus 255 YPs~~ek~~LA~~tgLs~kQI~nWF~N 281 (303)
-+++..|..||..+|++.+.|..|-.-
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~~~ 52 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWVNQ 52 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHhH
Confidence 388899999999999999999999543
No 182
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=23.68 E-value=67 Score=34.30 Aligned_cols=58 Identities=24% Similarity=0.409 Sum_probs=49.7
Q ss_pred hhccCCCCCcchHHHHHHHHHHcCCCCCCCHHH---HHHHHHHhCCChHHHhhhhHhhhhhcc
Q 022056 228 RKRRAGKLPGDTTSVLKNWWQQHSKWPYPTEDD---KAKLVEETGLQLKQINNWFINQRKRNW 287 (303)
Q Consensus 228 kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs~~e---k~~LA~~tgLs~kQI~nWF~N~R~R~k 287 (303)
+++++.++..+...+|..+...-. -||.... -..|+..+.+..+.|.-.|+|+|.-.+
T Consensus 647 ~p~~~~~isge~~~~~qs~i~~~g--l~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~ 707 (769)
T KOG3755|consen 647 KPRKRTKISGEALGILQSFITDVG--LYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVK 707 (769)
T ss_pred CccccceecccchHHHHHHHHHhc--cCchhhcccccchhhhhhcccHHHHHHhhhcceeecc
Confidence 566778899999999999877654 6999888 889999999999999999999986544
No 183
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=23.53 E-value=70 Score=23.35 Aligned_cols=19 Identities=21% Similarity=0.447 Sum_probs=16.9
Q ss_pred HHHHHHhCCChHHHhhhhH
Q 022056 262 AKLVEETGLQLKQINNWFI 280 (303)
Q Consensus 262 ~~LA~~tgLs~kQI~nWF~ 280 (303)
..+|+.+|++.+.|.+|-.
T Consensus 17 ~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 17 KEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHCCChHHHHHHHH
Confidence 4799999999999999954
No 184
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=23.28 E-value=66 Score=23.18 Aligned_cols=20 Identities=10% Similarity=0.182 Sum_probs=17.4
Q ss_pred HHHHHHhCCChHHHhhhhHh
Q 022056 262 AKLVEETGLQLKQINNWFIN 281 (303)
Q Consensus 262 ~~LA~~tgLs~kQI~nWF~N 281 (303)
.++|+.+|+++++|..|-.+
T Consensus 4 ~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 46899999999999999654
No 185
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=23.27 E-value=46 Score=28.77 Aligned_cols=47 Identities=4% Similarity=-0.021 Sum_probs=36.8
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||+..++++.-.+.... + -.++|..+|++...|.++....|.+.++.
T Consensus 135 L~~~~r~v~~l~~~~g~--s------~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 135 VNPIDREILVLRFVAEL--E------FQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred cChhheeeeeeHHhcCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 77777777765544442 2 26899999999999999999999988763
No 186
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=23.21 E-value=85 Score=29.01 Aligned_cols=48 Identities=13% Similarity=0.077 Sum_probs=39.0
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.||...+.+|...|... -.-..+|..+|++...|..+..-.+++.++-
T Consensus 203 ~L~~~~r~vl~l~y~~~--------~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 203 QLEERTREVLEFVFLHD--------LTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred cCCHHHHHHHHHHHHCC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 37888888988777654 2346899999999999999999999988754
No 187
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=22.49 E-value=63 Score=22.86 Aligned_cols=23 Identities=22% Similarity=0.299 Sum_probs=19.2
Q ss_pred HHHHHHHhCCChHHHhhhhHhhh
Q 022056 261 KAKLVEETGLQLKQINNWFINQR 283 (303)
Q Consensus 261 k~~LA~~tgLs~kQI~nWF~N~R 283 (303)
...+|+.+|++..+|..|-.+.|
T Consensus 15 ~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 15 QKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHHCcCHHHHHHHHCCCc
Confidence 45789999999999999998855
No 188
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=22.35 E-value=48 Score=29.94 Aligned_cols=47 Identities=15% Similarity=0.124 Sum_probs=37.6
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
||...+.++.-.+... ..-.++|+.+|++...|.+.....|.+.++-
T Consensus 150 L~~~~r~i~~l~~~~g--------~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~ 196 (231)
T PRK11922 150 LPDAFRAVFVLRVVEE--------LSVEETAQALGLPEETVKTRLHRARRLLRES 196 (231)
T ss_pred CCHHHhhhheeehhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 7888888876654433 3345899999999999999999999998875
No 189
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=22.27 E-value=98 Score=26.95 Aligned_cols=48 Identities=10% Similarity=-0.028 Sum_probs=39.8
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
||...+.++.-.+..+. + -.++|..+|++...|.++..-.|++.++..
T Consensus 129 Lp~~~r~v~~l~~~~g~----s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 129 LDPEYREPLLLQVIGGF----S----GEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred CCHHHHHHHHHHHHhCC----C----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 88888899887777763 2 347899999999999999999999888753
No 190
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=22.26 E-value=93 Score=28.24 Aligned_cols=52 Identities=12% Similarity=0.093 Sum_probs=40.6
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
||...+.+|.-.|.-+. -..-.-..+|+.+|++...|+.+....+++.|+..
T Consensus 177 L~~~er~vl~l~ygl~~----~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~ 228 (238)
T TIGR02393 177 LTERERKVLRMRYGLLD----GRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPS 228 (238)
T ss_pred CCHHHHHHHHHHhCCCC----CCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhH
Confidence 88888899988763221 11234668999999999999999999999999763
No 191
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=22.21 E-value=1.1e+02 Score=26.17 Aligned_cols=28 Identities=11% Similarity=0.139 Sum_probs=24.9
Q ss_pred HHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 261 KAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 261 k~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
-..+|+.+|++...|.+++.-.|++.++
T Consensus 168 ~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 168 YQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4579999999999999999999998875
No 192
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=22.07 E-value=79 Score=25.91 Aligned_cols=46 Identities=20% Similarity=0.159 Sum_probs=35.4
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
||...+.++.-.+... ..-.++|+.+|+++..|.++..-.|++.++
T Consensus 106 L~~~~r~i~~l~~~~g--------~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 106 LPENYRTVLILREFKE--------FSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred CCHhheeeeeehhhcc--------CcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6777777775543334 234589999999999999999999998775
No 193
>PF07042 TrfA: TrfA protein; InterPro: IPR010751 This family consists of several bacterial TrfA proteins. The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa [].
Probab=22.07 E-value=1.2e+02 Score=29.33 Aligned_cols=48 Identities=23% Similarity=0.416 Sum_probs=36.6
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhh
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRK 284 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~ 284 (303)
.|+....+-|-.+|..| ..|||-.-++.. ..||-..+++.+|=++-++
T Consensus 210 ~L~~~lA~wLh~yyaSH-~~P~P~kvetl~--~lcGS~~~~l~~FR~~Lk~ 257 (282)
T PF07042_consen 210 KLSPRLAKWLHGYYASH-KKPYPIKVETLR--ELCGSESSRLRKFRQQLKK 257 (282)
T ss_pred hcCcHHHHHHHHHHhcC-CCCCCccHHHHH--HHcCCCccCHHHHHHHHHH
Confidence 36665567788999999 579999887544 4688888899998777654
No 194
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=22.04 E-value=1.3e+02 Score=19.93 Aligned_cols=30 Identities=10% Similarity=0.148 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 260 DKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 260 ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
....+|+.++++...|..|....+++...+
T Consensus 17 s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 346789999999999999998777766543
No 195
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=21.92 E-value=77 Score=22.62 Aligned_cols=19 Identities=16% Similarity=0.345 Sum_probs=17.1
Q ss_pred HHHHHHhCCChHHHhhhhH
Q 022056 262 AKLVEETGLQLKQINNWFI 280 (303)
Q Consensus 262 ~~LA~~tgLs~kQI~nWF~ 280 (303)
..+|+.+|++...|.+|-.
T Consensus 4 ~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 4 GAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999975
No 196
>PF02290 SRP14: Signal recognition particle 14kD protein; InterPro: IPR003210 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the 14 kDa SRP14 component. Both SRP9 and SRP14 have the same (beta)-alpha-beta(3)-alpha fold. The heterodimer has pseudo two-fold symmetry and is saddle-like, consisting of a curved six-stranded beta-sheet that has four helices packed on the convex side and an exposed concave surface lined with positively charged residues. The SRP9/SRP14 heterodimer is essential for SRP RNA binding, mediating the pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP [].; GO: 0008312 7S RNA binding, 0030942 endoplasmic reticulum signal peptide binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0005786 signal recognition particle, endoplasmic reticulum targeting; PDB: 1914_A 1RY1_D 1E8O_B 2W9J_B.
Probab=21.91 E-value=66 Score=25.70 Aligned_cols=19 Identities=32% Similarity=0.496 Sum_probs=16.1
Q ss_pred CCchHHHHHHHHHHHHHHH
Q 022056 100 HERQELDNFLAQYLIVLCT 118 (303)
Q Consensus 100 ~~dpELDqFMeaYc~vL~k 118 (303)
-...+|+.|..+|+.||..
T Consensus 70 V~~~~l~~F~~~Y~~v~K~ 88 (93)
T PF02290_consen 70 VDPDDLDKFWQSYANVLKA 88 (93)
T ss_dssp EETTCHHHHHHHHHHHHHH
T ss_pred ECHHHHHHHHHHHHHHHHh
Confidence 3558999999999999864
No 197
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=21.85 E-value=77 Score=26.71 Aligned_cols=48 Identities=13% Similarity=0.143 Sum_probs=38.1
Q ss_pred CCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccccC
Q 022056 235 LPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHSN 290 (303)
Q Consensus 235 lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~~ 290 (303)
||...+.+|.-.+... ++ -..+|+.+|++...|.+.+...|++.++-.
T Consensus 121 L~~~~r~vl~l~~~~g----~s----~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 121 LSLEHRAVLVLHDLED----LP----QKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred CCHHHeeeeeehHhcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 7777888887655444 23 458999999999999999999999988653
No 198
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=21.73 E-value=81 Score=28.47 Aligned_cols=52 Identities=10% Similarity=0.130 Sum_probs=37.0
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.||...+.++.-.|..+. -....-..+|..+|++...|.++-..+|++.++.
T Consensus 175 ~Lp~~~R~i~~l~y~~~~----~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGN----GKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred hCCHHHHHHHHHHhCCCC----CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 388889999877552110 0112345799999999999999988888877653
No 199
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=21.28 E-value=1.2e+02 Score=26.08 Aligned_cols=48 Identities=8% Similarity=-0.013 Sum_probs=38.2
Q ss_pred CCCCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 232 AGKLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 232 r~~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
.+.||..++++|.- +... + .-.++|+..|+|...|.+|-...|++.++
T Consensus 4 ~~~Lte~qr~VL~L-r~~G----l----Tq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLEL-REKG----L----SQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHH-HHcC----C----CHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 35688888888866 3333 2 45689999999999999999999999885
No 200
>PRK05572 sporulation sigma factor SigF; Validated
Probab=20.77 E-value=99 Score=28.31 Aligned_cols=48 Identities=8% Similarity=0.085 Sum_probs=38.9
Q ss_pred CCCcchHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 234 KLPGDTTSVLKNWWQQHSKWPYPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 234 ~lpk~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
.||...+.++...|... ..-..+|+.+|+++..|..+-....++.++.
T Consensus 202 ~L~~~~~~v~~l~~~~~--------~s~~eIA~~lgis~~~V~~~~~ral~kLr~~ 249 (252)
T PRK05572 202 ELDERERLIVYLRYFKD--------KTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249 (252)
T ss_pred cCCHHHHHHHHHHHhCC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 38888999987766543 3456899999999999999999988887753
No 201
>PF12323 HTH_OrfB_IS605: Helix-turn-helix domain; InterPro: IPR021027 This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases [, , ]. It is usually associated with PF01385 from PFAM and PF07282 from PFAM.
Probab=20.68 E-value=93 Score=21.09 Aligned_cols=34 Identities=29% Similarity=0.596 Sum_probs=26.7
Q ss_pred CCCHHHHHHHHHHhCCChHHHhhhhHhhhhhcccc
Q 022056 255 YPTEDDKAKLVEETGLQLKQINNWFINQRKRNWHS 289 (303)
Q Consensus 255 YPs~~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk~ 289 (303)
|||.+++..|.+..|.. ..|=||....|...++.
T Consensus 10 ~Pt~~Q~~~L~~~~~~~-R~vyN~~L~~~~~~y~~ 43 (46)
T PF12323_consen 10 YPTKEQEEKLERWFGAC-RFVYNWALAERKEAYKQ 43 (46)
T ss_pred ecCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH
Confidence 89999999998888764 56788888888776653
No 202
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=20.61 E-value=1.3e+02 Score=19.82 Aligned_cols=27 Identities=30% Similarity=0.562 Sum_probs=17.9
Q ss_pred chHHHHHHHHHHcCCCCCCCHH-HHHHHH
Q 022056 238 DTTSVLKNWWQQHSKWPYPTED-DKAKLV 265 (303)
Q Consensus 238 ~~~~~L~~wf~~h~~~PYPs~~-ek~~LA 265 (303)
-...-|+.|+..| ..|+|... .|..|.
T Consensus 4 Ws~~~L~~wL~~~-gi~~~~~~~~rd~Ll 31 (38)
T PF10281_consen 4 WSDSDLKSWLKSH-GIPVPKSAKTRDELL 31 (38)
T ss_pred CCHHHHHHHHHHc-CCCCCCCCCCHHHHH
Confidence 3567899999988 35666444 555553
No 203
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=20.44 E-value=1.3e+02 Score=25.91 Aligned_cols=30 Identities=30% Similarity=0.347 Sum_probs=23.5
Q ss_pred HHHHHHHHHhCCChHHHhhhhHhhhhhccc
Q 022056 259 DDKAKLVEETGLQLKQINNWFINQRKRNWH 288 (303)
Q Consensus 259 ~ek~~LA~~tgLs~kQI~nWF~N~R~R~kk 288 (303)
+.-..+++.||.+.++|..|.---|--.+.
T Consensus 47 ati~eV~e~tgVs~~~I~~~IreGRL~~~~ 76 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIREGRLQLKH 76 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCeeccC
Confidence 455689999999999999998766654443
No 204
>KOG4511 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.44 E-value=1.3e+02 Score=29.29 Aligned_cols=27 Identities=30% Similarity=0.395 Sum_probs=22.8
Q ss_pred HHHhCCChHHHHHHHHhh--hcccCCCcc
Q 022056 39 EIASHPLYEQLLAAHVSC--LRVATPIDQ 65 (303)
Q Consensus 39 ~I~sHPlYp~Ll~A~i~C--~KVgaP~e~ 65 (303)
=|+.|-=|..|+.-.++| --||.-|+.
T Consensus 50 y~~IH~EYk~LVd~lle~f~eevgi~p~q 78 (335)
T KOG4511|consen 50 YIMIHKEYKQLVDTLLECFCEEVGITPTQ 78 (335)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCHHH
Confidence 478899999999999996 568888864
No 205
>PF13551 HTH_29: Winged helix-turn helix
Probab=20.35 E-value=1e+02 Score=23.75 Aligned_cols=27 Identities=15% Similarity=0.421 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhhhhc
Q 022056 260 DKAKLVEETGLQLKQINNWFINQRKRN 286 (303)
Q Consensus 260 ek~~LA~~tgLs~kQI~nWF~N~R~R~ 286 (303)
....+|+.+|++...|.+|....+..-
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 466899999999999999998866543
No 206
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=20.05 E-value=82 Score=27.32 Aligned_cols=30 Identities=13% Similarity=0.199 Sum_probs=22.5
Q ss_pred HhhccCCCCCcchHHHHHHHHHHcCCCCCCC
Q 022056 227 LRKRRAGKLPGDTTSVLKNWWQQHSKWPYPT 257 (303)
Q Consensus 227 ~kkrkr~~lpk~~~~~L~~wf~~h~~~PYPs 257 (303)
....+-+.|+.++...|..+... ...++|+
T Consensus 44 ~~~~~~~~Lt~~qi~~l~~~i~~-~~~~iP~ 73 (144)
T TIGR03629 44 DPNAKLGYLDDEEIEKLEEAVEN-YEYGIPS 73 (144)
T ss_pred CCCCCcccCCHHHHHHHHHHHHh-ccccCCH
Confidence 34556688999999999999876 5555555
Done!